Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 00:15:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/10_2023/7k24_22642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/10_2023/7k24_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_22642/10_2023/7k24_22642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/10_2023/7k24_22642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/10_2023/7k24_22642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/10_2023/7k24_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 7.38, per 1000 atoms: 0.54 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: 5.35 Conformation dependent library (CDL) restraints added in 2.0 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: 4.26 Time building geometry restraints manager: 5.75 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: 1.560 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: 6.630 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.210 Find NCS groups from input model: 0.850 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: 0.020 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.590 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 33 residues processed: 435 average time/residue: 1.2247 time to fit residues: 582.4068 Evaluate side-chains 276 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 9 average time/residue: 0.4461 time to fit residues: 7.1731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 0.0030 chunk 102 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- 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 339 GLN F1 347 GLN F2 54 ASN ** F2 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 339 GLN F5 347 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1814 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= 0.240 Angle : 0.628 7.694 19230 Z= 0.317 Chirality : 0.043 0.131 2155 Planarity : 0.005 0.044 2510 Dihedral : 5.594 23.366 1890 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 8.55 % Allowed : 22.32 % 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: -2.68 (0.18), residues: 1755 helix: -2.87 (0.43), residues: 120 sheet: -0.14 (0.24), residues: 450 loop : -2.51 (0.16), residues: 1185 *********************** 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 384 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 251 time to evaluate : 1.632 Fit side-chains revert: symmetry clash outliers start: 133 outliers final: 65 residues processed: 332 average time/residue: 0.8977 time to fit residues: 330.3089 Evaluate side-chains 295 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 230 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 43 residues processed: 22 average time/residue: 0.3192 time to fit residues: 11.6462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 171 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 92 ASN F1 149 ASN ** F2 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 104 GLN F3 80 ASN F3 92 ASN F3 104 GLN F3 206 GLN F3 254 GLN ** F4 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 104 GLN F4 345 ASN F5 92 ASN F5 104 GLN F5 254 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14090 Z= 0.165 Angle : 0.554 5.871 19230 Z= 0.277 Chirality : 0.041 0.127 2155 Planarity : 0.005 0.036 2510 Dihedral : 4.955 21.792 1890 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.11 % Allowed : 25.34 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.19), residues: 1755 helix: -1.29 (0.54), residues: 85 sheet: 0.12 (0.24), residues: 450 loop : -2.08 (0.17), residues: 1220 *********************** 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 341 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 246 time to evaluate : 1.729 Fit side-chains revert: symmetry clash outliers start: 95 outliers final: 51 residues processed: 314 average time/residue: 0.8876 time to fit residues: 309.6434 Evaluate side-chains 282 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 44 residues processed: 7 average time/residue: 0.4547 time to fit residues: 5.4045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 92 ASN F2 317 ASN F3 80 ASN ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 92 ASN ** F4 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 345 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14090 Z= 0.211 Angle : 0.577 5.803 19230 Z= 0.287 Chirality : 0.042 0.126 2155 Planarity : 0.005 0.035 2510 Dihedral : 5.051 20.867 1890 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 6.56 % Allowed : 25.21 % Favored : 68.23 % 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: -1.75 (0.19), residues: 1755 helix: -0.60 (0.53), residues: 85 sheet: 0.32 (0.24), residues: 450 loop : -1.94 (0.17), residues: 1220 *********************** 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 338 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 236 time to evaluate : 1.616 Fit side-chains revert: symmetry clash outliers start: 102 outliers final: 70 residues processed: 306 average time/residue: 1.0228 time to fit residues: 348.8195 Evaluate side-chains 293 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 223 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 51 residues processed: 19 average time/residue: 0.2766 time to fit residues: 9.6211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 92 ASN F1 149 ASN F1 345 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 92 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 92 ASN ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 92 ASN F4 161 GLN F4 345 ASN F5 92 ASN F5 254 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 14090 Z= 0.521 Angle : 0.774 7.486 19230 Z= 0.386 Chirality : 0.050 0.144 2155 Planarity : 0.006 0.044 2510 Dihedral : 6.084 29.204 1890 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 7.78 % Allowed : 24.24 % Favored : 67.97 % 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: -2.09 (0.19), residues: 1755 helix: -1.69 (0.45), residues: 120 sheet: 0.19 (0.24), residues: 460 loop : -2.18 (0.17), residues: 1175 *********************** 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 349 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 228 time to evaluate : 1.741 Fit side-chains revert: symmetry clash outliers start: 121 outliers final: 82 residues processed: 306 average time/residue: 1.1617 time to fit residues: 391.7008 Evaluate side-chains 301 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 219 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 56 residues processed: 26 average time/residue: 0.3057 time to fit residues: 13.0313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.2980 chunk 152 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** ** F3 71 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14090 Z= 0.274 Angle : 0.628 6.978 19230 Z= 0.315 Chirality : 0.044 0.137 2155 Planarity : 0.005 0.042 2510 Dihedral : 5.524 23.792 1890 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.21 % Allowed : 26.62 % Favored : 68.17 % 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 (0.20), residues: 1755 helix: 0.18 (0.58), residues: 85 sheet: 0.33 (0.25), residues: 460 loop : -1.91 (0.17), residues: 1210 *********************** 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 302 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 221 time to evaluate : 1.627 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 60 residues processed: 284 average time/residue: 1.1066 time to fit residues: 348.3818 Evaluate side-chains 274 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 214 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 54 residues processed: 6 average time/residue: 0.3236 time to fit residues: 4.7848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 95 optimal weight: 0.0000 chunk 142 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 92 ASN F1 149 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 206 GLN F3 345 ASN ** F4 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8157 moved from start: 0.2677 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= 0.168 Angle : 0.545 7.289 19230 Z= 0.272 Chirality : 0.041 0.138 2155 Planarity : 0.005 0.034 2510 Dihedral : 4.862 19.076 1890 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.08 % Allowed : 27.14 % Favored : 67.78 % 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: -1.32 (0.20), residues: 1755 helix: 0.65 (0.60), residues: 85 sheet: 0.65 (0.25), residues: 450 loop : -1.73 (0.17), residues: 1220 *********************** 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 311 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 232 time to evaluate : 1.672 Fit side-chains outliers start: 79 outliers final: 50 residues processed: 298 average time/residue: 1.0593 time to fit residues: 350.6431 Evaluate side-chains 270 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 0.1322 time to fit residues: 3.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 92 ASN ** F3 71 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2717 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= 0.194 Angle : 0.563 7.266 19230 Z= 0.280 Chirality : 0.042 0.126 2155 Planarity : 0.005 0.030 2510 Dihedral : 4.894 19.550 1890 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.24 % Allowed : 27.85 % Favored : 67.91 % 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: -1.18 (0.20), residues: 1755 helix: 0.86 (0.61), residues: 85 sheet: 0.70 (0.25), residues: 450 loop : -1.62 (0.17), residues: 1220 *********************** 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 286 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 220 time to evaluate : 1.764 Fit side-chains outliers start: 66 outliers final: 50 residues processed: 276 average time/residue: 1.1346 time to fit residues: 346.7727 Evaluate side-chains 266 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 47 residues processed: 3 average time/residue: 0.1881 time to fit residues: 3.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 5.9990 chunk 147 optimal weight: 0.1980 chunk 157 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 142 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 254 GLN F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 161 GLN F4 242 ASN F4 345 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2623 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= 0.300 Angle : 0.634 7.183 19230 Z= 0.316 Chirality : 0.044 0.131 2155 Planarity : 0.005 0.034 2510 Dihedral : 5.343 23.936 1890 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.99 % Allowed : 28.30 % Favored : 67.72 % 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: -1.23 (0.20), residues: 1755 helix: 0.83 (0.60), residues: 85 sheet: 0.68 (0.25), residues: 450 loop : -1.65 (0.17), residues: 1220 *********************** 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 284 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 222 time to evaluate : 1.650 Fit side-chains outliers start: 62 outliers final: 52 residues processed: 275 average time/residue: 1.1738 time to fit residues: 355.6466 Evaluate side-chains 269 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 49 residues processed: 3 average time/residue: 0.6000 time to fit residues: 4.4539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 0.0000 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN F4 161 GLN F4 242 ASN F4 345 ASN F5 254 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2703 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= 0.216 Angle : 0.586 7.577 19230 Z= 0.291 Chirality : 0.042 0.127 2155 Planarity : 0.005 0.031 2510 Dihedral : 5.072 21.414 1890 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.67 % Allowed : 28.87 % Favored : 67.46 % 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: -1.14 (0.20), residues: 1755 helix: 0.94 (0.61), residues: 85 sheet: 0.72 (0.25), residues: 450 loop : -1.58 (0.17), residues: 1220 ********************** 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: 57 poor density : 214 time to evaluate : 1.655 Fit side-chains outliers start: 57 outliers final: 51 residues processed: 268 average time/residue: 1.1395 time to fit residues: 336.7921 Evaluate side-chains 262 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 50 residues processed: 1 average time/residue: 0.2543 time to fit residues: 2.4469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 139 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 0.0030 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.1686 ------------------------------------------------------------------------------- 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** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 92 ASN F3 345 ASN ** F4 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 242 ASN F4 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.151655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.123135 restraints weight = 13967.225| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.59 r_work: 0.3058 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14090 Z= 0.155 Angle : 0.525 7.455 19230 Z= 0.260 Chirality : 0.040 0.132 2155 Planarity : 0.004 0.029 2510 Dihedral : 4.359 19.022 1890 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.47 % Allowed : 29.07 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1755 helix: 1.41 (0.63), residues: 85 sheet: 0.75 (0.25), residues: 450 loop : -1.41 (0.18), residues: 1220 =============================================================================== Job complete usr+sys time: 5778.20 seconds wall clock time: 102 minutes 45.24 seconds (6165.24 seconds total)