Starting phenix.real_space_refine on Sun Mar 17 19:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxp_13103/03_2024/7oxp_13103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxp_13103/03_2024/7oxp_13103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxp_13103/03_2024/7oxp_13103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxp_13103/03_2024/7oxp_13103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxp_13103/03_2024/7oxp_13103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxp_13103/03_2024/7oxp_13103.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 90 5.16 5 C 12130 2.51 5 N 3080 2.21 5 O 3430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 48": "OD1" <-> "OD2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "I PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 48": "OD1" <-> "OD2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18730 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "C" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "F" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "H" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "I" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "J" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 9.76, per 1000 atoms: 0.52 Number of scatterers: 18730 At special positions: 0 Unit cell: (152.07, 157.002, 83.844, 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 90 16.00 O 3430 8.00 N 3080 7.00 C 12130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 159 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 159 " distance=2.03 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: 7.87 Conformation dependent library (CDL) restraints added in 3.8 seconds 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 32.2% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.889A pdb=" N LEU B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 243 through 255 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.891A pdb=" N LEU C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 235 through 243 Processing helix chain 'D' and resid 243 through 255 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 235 through 243 Processing helix chain 'E' and resid 243 through 255 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE F 36 " --> pdb=" O LEU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 177 through 186 Processing helix chain 'F' and resid 235 through 243 Processing helix chain 'F' and resid 243 through 255 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE F 263 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.744A pdb=" N ILE G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 235 through 243 Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU G 262 " --> pdb=" O ILE G 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE G 263 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 177 through 186 Processing helix chain 'H' and resid 235 through 243 Processing helix chain 'H' and resid 243 through 255 Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU H 262 " --> pdb=" O ILE H 258 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE H 263 " --> pdb=" O ILE H 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE I 36 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 243 through 255 Processing helix chain 'I' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU I 262 " --> pdb=" O ILE I 258 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE I 263 " --> pdb=" O ILE I 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 177 through 186 Processing helix chain 'J' and resid 235 through 243 Processing helix chain 'J' and resid 243 through 255 Processing helix chain 'J' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU J 262 " --> pdb=" O ILE J 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE J 263 " --> pdb=" O ILE J 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 54 current: chain 'A' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE A 77 " --> pdb=" O MET A 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 95 through 98 current: chain 'A' and resid 148 through 160 Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 54 current: chain 'B' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE B 77 " --> pdb=" O MET B 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 95 through 98 current: chain 'B' and resid 148 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 54 current: chain 'C' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE C 77 " --> pdb=" O MET C 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 95 through 98 current: chain 'C' and resid 148 through 160 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 54 current: chain 'D' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE D 77 " --> pdb=" O MET D 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 98 current: chain 'D' and resid 148 through 160 Processing sheet with id=AA5, first strand: chain 'E' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 54 current: chain 'E' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE E 77 " --> pdb=" O MET E 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 95 through 98 current: chain 'E' and resid 148 through 160 Processing sheet with id=AA6, first strand: chain 'F' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 54 current: chain 'F' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE F 77 " --> pdb=" O MET F 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 95 through 98 current: chain 'F' and resid 148 through 160 Processing sheet with id=AA7, first strand: chain 'G' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 50 through 54 current: chain 'G' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE G 77 " --> pdb=" O MET G 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 95 through 98 current: chain 'G' and resid 148 through 160 Processing sheet with id=AA8, first strand: chain 'H' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 50 through 54 current: chain 'H' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE H 77 " --> pdb=" O MET H 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 95 through 98 current: chain 'H' and resid 148 through 160 Processing sheet with id=AA9, first strand: chain 'I' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 50 through 54 current: chain 'I' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE I 77 " --> pdb=" O MET I 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 95 through 98 current: chain 'I' and resid 148 through 160 Processing sheet with id=AB1, first strand: chain 'J' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 50 through 54 current: chain 'J' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE J 77 " --> pdb=" O MET J 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 95 through 98 current: chain 'J' and resid 148 through 160 440 hydrogen bonds defined for protein. 1290 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: 4.46 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6000 1.34 - 1.46: 3958 1.46 - 1.58: 8992 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 19090 Sorted by residual: bond pdb=" N HIS F 119 " pdb=" CA HIS F 119 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.86e-01 bond pdb=" N HIS G 119 " pdb=" CA HIS G 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.51e-01 bond pdb=" N HIS B 119 " pdb=" CA HIS B 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.51e-01 bond pdb=" N HIS A 119 " pdb=" CA HIS A 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.46e-01 bond pdb=" N HIS D 119 " pdb=" CA HIS D 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.40e-01 ... (remaining 19085 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 549 107.15 - 113.85: 10949 113.85 - 120.55: 7280 120.55 - 127.26: 6912 127.26 - 133.96: 150 Bond angle restraints: 25840 Sorted by residual: angle pdb=" CA LEU G 30 " pdb=" CB LEU G 30 " pdb=" CG LEU G 30 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 angle pdb=" CA LEU D 30 " pdb=" CB LEU D 30 " pdb=" CG LEU D 30 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" CA LEU F 30 " pdb=" CB LEU F 30 " pdb=" CG LEU F 30 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" CA LEU A 30 " pdb=" CB LEU A 30 " pdb=" CG LEU A 30 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 angle pdb=" CA LEU I 30 " pdb=" CB LEU I 30 " pdb=" CG LEU I 30 " ideal model delta sigma weight residual 116.30 124.26 -7.96 3.50e+00 8.16e-02 5.18e+00 ... (remaining 25835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 10540 16.59 - 33.18: 870 33.18 - 49.77: 190 49.77 - 66.36: 30 66.36 - 82.95: 30 Dihedral angle restraints: 11660 sinusoidal: 4880 harmonic: 6780 Sorted by residual: dihedral pdb=" CB GLU I 185 " pdb=" CG GLU I 185 " pdb=" CD GLU I 185 " pdb=" OE1 GLU I 185 " ideal model delta sinusoidal sigma weight residual 0.00 -82.95 82.95 1 3.00e+01 1.11e-03 9.36e+00 dihedral pdb=" CB GLU J 185 " pdb=" CG GLU J 185 " pdb=" CD GLU J 185 " pdb=" OE1 GLU J 185 " ideal model delta sinusoidal sigma weight residual 0.00 -82.92 82.92 1 3.00e+01 1.11e-03 9.35e+00 dihedral pdb=" CB GLU A 185 " pdb=" CG GLU A 185 " pdb=" CD GLU A 185 " pdb=" OE1 GLU A 185 " ideal model delta sinusoidal sigma weight residual 0.00 -82.89 82.89 1 3.00e+01 1.11e-03 9.35e+00 ... (remaining 11657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1683 0.025 - 0.050: 770 0.050 - 0.076: 321 0.076 - 0.101: 140 0.101 - 0.126: 116 Chirality restraints: 3030 Sorted by residual: chirality pdb=" CA ILE I 95 " pdb=" N ILE I 95 " pdb=" C ILE I 95 " pdb=" CB ILE I 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE B 95 " pdb=" N ILE B 95 " pdb=" C ILE B 95 " pdb=" CB ILE B 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE J 95 " pdb=" N ILE J 95 " pdb=" C ILE J 95 " pdb=" CB ILE J 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 3027 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 95 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO B 96 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 95 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO E 96 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 95 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO H 96 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 96 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 96 " -0.017 5.00e-02 4.00e+02 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 312 2.68 - 3.23: 17062 3.23 - 3.79: 28768 3.79 - 4.34: 40978 4.34 - 4.90: 66546 Nonbonded interactions: 153666 Sorted by model distance: nonbonded pdb=" OE2 GLU H 102 " pdb=" OG SER H 197 " model vdw 2.120 2.440 nonbonded pdb=" OE2 GLU C 102 " pdb=" OG SER C 197 " model vdw 2.121 2.440 nonbonded pdb=" OE2 GLU F 102 " pdb=" OG SER F 197 " model vdw 2.121 2.440 nonbonded pdb=" OE2 GLU G 102 " pdb=" OG SER G 197 " model vdw 2.121 2.440 nonbonded pdb=" OE2 GLU B 102 " pdb=" OG SER B 197 " model vdw 2.121 2.440 ... (remaining 153661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.780 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 49.870 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 84.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.003 0.023 19090 Z= 0.168 Angle : 0.585 7.989 25840 Z= 0.306 Chirality : 0.042 0.126 3030 Planarity : 0.004 0.030 3260 Dihedral : 13.631 82.946 7210 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 0.08 (0.18), residues: 2260 helix: 0.23 (0.21), residues: 620 sheet: 0.38 (0.17), residues: 890 loop : -0.28 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 186 HIS 0.003 0.001 HIS A 38 PHE 0.008 0.001 PHE I 58 TYR 0.018 0.002 TYR J 248 ARG 0.004 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 2.427 Fit side-chains REVERT: A 42 LEU cc_start: 0.8395 (mm) cc_final: 0.8098 (mm) REVERT: B 169 GLN cc_start: 0.7771 (mp10) cc_final: 0.7548 (mp10) REVERT: C 42 LEU cc_start: 0.8327 (mm) cc_final: 0.8058 (mm) REVERT: D 42 LEU cc_start: 0.8508 (mm) cc_final: 0.8234 (mm) REVERT: D 240 MET cc_start: 0.8483 (mtm) cc_final: 0.8270 (mtm) REVERT: G 42 LEU cc_start: 0.8447 (mm) cc_final: 0.8148 (mm) REVERT: H 42 LEU cc_start: 0.8351 (mm) cc_final: 0.8078 (mm) REVERT: I 42 LEU cc_start: 0.8423 (mm) cc_final: 0.8137 (mm) REVERT: I 110 GLN cc_start: 0.8536 (mt0) cc_final: 0.8332 (mt0) REVERT: I 215 GLN cc_start: 0.7650 (mm110) cc_final: 0.7279 (mp-120) REVERT: J 42 LEU cc_start: 0.8542 (mm) cc_final: 0.8263 (mm) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 1.8058 time to fit residues: 843.9753 Evaluate side-chains 364 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 85 GLN A 173 GLN B 85 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 85 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 72 GLN D 85 GLN D 110 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 85 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 85 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN G 85 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 85 GLN H 110 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN I 72 GLN I 85 GLN I 173 GLN J 85 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19090 Z= 0.423 Angle : 0.642 8.237 25840 Z= 0.314 Chirality : 0.045 0.135 3030 Planarity : 0.004 0.035 3260 Dihedral : 4.853 15.853 2470 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.33 % Allowed : 11.24 % Favored : 87.43 % 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: 0.05 (0.17), residues: 2260 helix: -0.17 (0.19), residues: 640 sheet: 0.54 (0.17), residues: 910 loop : -0.18 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 186 HIS 0.005 0.002 HIS I 152 PHE 0.018 0.002 PHE G 70 TYR 0.013 0.002 TYR G 202 ARG 0.006 0.001 ARG J 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 321 time to evaluate : 2.005 Fit side-chains REVERT: C 42 LEU cc_start: 0.8416 (mm) cc_final: 0.8131 (mm) REVERT: C 227 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8499 (ttpp) REVERT: C 244 ARG cc_start: 0.7550 (tpp80) cc_final: 0.6674 (ttp-170) REVERT: D 42 LEU cc_start: 0.8433 (mm) cc_final: 0.8148 (mm) REVERT: D 227 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8571 (ttpp) REVERT: E 42 LEU cc_start: 0.8475 (mm) cc_final: 0.8231 (mm) REVERT: H 42 LEU cc_start: 0.8430 (mm) cc_final: 0.8136 (mm) REVERT: H 103 TYR cc_start: 0.9283 (m-80) cc_final: 0.8940 (m-80) REVERT: J 227 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8608 (ttpp) outliers start: 29 outliers final: 9 residues processed: 334 average time/residue: 1.8081 time to fit residues: 655.2074 Evaluate side-chains 276 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.0070 chunk 173 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 chunk 71 optimal weight: 0.3980 chunk 167 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 85 GLN A 121 ASN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 56 ASN C 85 GLN C 121 ASN C 173 GLN D 85 GLN D 121 ASN D 173 GLN E 85 GLN E 121 ASN F 56 ASN F 85 GLN F 121 ASN G 85 GLN G 121 ASN G 173 GLN H 56 ASN H 85 GLN H 121 ASN H 173 GLN I 56 ASN I 85 GLN I 121 ASN I 173 GLN J 85 GLN J 121 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 19090 Z= 0.163 Angle : 0.512 8.167 25840 Z= 0.250 Chirality : 0.041 0.128 3030 Planarity : 0.003 0.026 3260 Dihedral : 4.241 12.198 2470 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 14.04 % Favored : 84.08 % 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: 0.34 (0.18), residues: 2260 helix: 0.13 (0.20), residues: 640 sheet: 0.68 (0.17), residues: 910 loop : -0.04 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 186 HIS 0.002 0.001 HIS E 221 PHE 0.008 0.001 PHE C 245 TYR 0.011 0.001 TYR B 182 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 1.869 Fit side-chains REVERT: C 227 LYS cc_start: 0.8851 (ttpp) cc_final: 0.8613 (ttmt) REVERT: C 244 ARG cc_start: 0.7435 (tpp80) cc_final: 0.6576 (ttp-170) REVERT: D 42 LEU cc_start: 0.8314 (mm) cc_final: 0.8039 (mm) REVERT: E 42 LEU cc_start: 0.8477 (mm) cc_final: 0.8191 (mm) REVERT: E 227 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8596 (ttpp) REVERT: G 179 LEU cc_start: 0.9018 (tp) cc_final: 0.8773 (tp) REVERT: H 42 LEU cc_start: 0.8352 (mm) cc_final: 0.8093 (mm) REVERT: I 110 GLN cc_start: 0.8535 (mt0) cc_final: 0.8269 (mt0) REVERT: I 215 GLN cc_start: 0.7685 (mp-120) cc_final: 0.6849 (mp-120) REVERT: I 244 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6650 (ttp80) REVERT: J 227 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8576 (ttpp) outliers start: 41 outliers final: 11 residues processed: 363 average time/residue: 1.6659 time to fit residues: 661.3409 Evaluate side-chains 314 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 300 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 30.0000 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN B 56 ASN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 56 ASN D 85 GLN D 173 GLN E 85 GLN E 173 GLN F 85 GLN F 121 ASN G 56 ASN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 173 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 19090 Z= 0.427 Angle : 0.619 8.096 25840 Z= 0.304 Chirality : 0.045 0.133 3030 Planarity : 0.004 0.044 3260 Dihedral : 4.823 13.638 2470 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.21 % Allowed : 15.64 % Favored : 81.15 % 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: 0.22 (0.17), residues: 2260 helix: 0.02 (0.19), residues: 640 sheet: 0.59 (0.17), residues: 910 loop : -0.07 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 186 HIS 0.004 0.002 HIS I 152 PHE 0.008 0.002 PHE A 71 TYR 0.012 0.002 TYR G 202 ARG 0.006 0.001 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 305 time to evaluate : 2.182 Fit side-chains REVERT: A 193 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: C 227 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8486 (ttpp) REVERT: D 42 LEU cc_start: 0.8321 (mm) cc_final: 0.8011 (mm) REVERT: D 227 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8575 (ttpp) REVERT: E 42 LEU cc_start: 0.8389 (mm) cc_final: 0.8120 (mm) REVERT: E 227 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8635 (ttpp) REVERT: F 193 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: G 193 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: H 103 TYR cc_start: 0.9298 (m-80) cc_final: 0.8995 (m-80) REVERT: H 227 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8545 (ttpp) REVERT: I 244 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6712 (ttp80) REVERT: J 227 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8635 (ttpp) outliers start: 70 outliers final: 17 residues processed: 352 average time/residue: 1.6458 time to fit residues: 632.6164 Evaluate side-chains 310 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 189 optimal weight: 0.0020 chunk 153 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN F 85 GLN F 121 ASN F 169 GLN F 173 GLN G 85 GLN G 121 ASN G 173 GLN H 56 ASN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN J 173 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19090 Z= 0.185 Angle : 0.521 8.356 25840 Z= 0.254 Chirality : 0.041 0.124 3030 Planarity : 0.003 0.026 3260 Dihedral : 4.321 12.513 2470 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.21 % Allowed : 17.06 % Favored : 79.72 % 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: 0.42 (0.18), residues: 2260 helix: 0.30 (0.20), residues: 640 sheet: 0.64 (0.17), residues: 910 loop : 0.02 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 186 HIS 0.002 0.001 HIS J 119 PHE 0.007 0.001 PHE C 71 TYR 0.009 0.001 TYR F 103 ARG 0.005 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 320 time to evaluate : 2.053 Fit side-chains REVERT: C 42 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7936 (mm) REVERT: C 227 LYS cc_start: 0.8852 (ttpp) cc_final: 0.8600 (ttmt) REVERT: E 42 LEU cc_start: 0.8359 (mm) cc_final: 0.8064 (mm) REVERT: H 42 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7994 (mm) REVERT: H 103 TYR cc_start: 0.9264 (m-80) cc_final: 0.8989 (m-80) REVERT: H 148 GLU cc_start: 0.7725 (pt0) cc_final: 0.7400 (pt0) REVERT: H 193 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7200 (mp0) REVERT: I 244 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7168 (ttt90) REVERT: J 102 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7638 (tm-30) REVERT: J 227 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8614 (ttpp) outliers start: 70 outliers final: 16 residues processed: 370 average time/residue: 1.5770 time to fit residues: 640.1710 Evaluate side-chains 317 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.8980 chunk 200 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 169 GLN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN F 121 ASN G 85 GLN G 121 ASN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN J 173 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19090 Z= 0.231 Angle : 0.539 8.297 25840 Z= 0.264 Chirality : 0.042 0.126 3030 Planarity : 0.003 0.029 3260 Dihedral : 4.322 13.209 2470 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.71 % Allowed : 17.71 % Favored : 79.59 % 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: 0.50 (0.18), residues: 2260 helix: 0.45 (0.20), residues: 640 sheet: 0.68 (0.17), residues: 910 loop : -0.01 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 186 HIS 0.003 0.001 HIS A 152 PHE 0.007 0.001 PHE I 71 TYR 0.009 0.001 TYR J 103 ARG 0.005 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 318 time to evaluate : 2.350 Fit side-chains REVERT: C 42 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7860 (mm) REVERT: C 227 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8594 (ttmt) REVERT: E 42 LEU cc_start: 0.8298 (mm) cc_final: 0.7994 (mm) REVERT: E 227 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8601 (ttpp) REVERT: H 42 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7893 (mm) REVERT: H 148 GLU cc_start: 0.7716 (pt0) cc_final: 0.7380 (pt0) REVERT: H 227 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8528 (ttpp) REVERT: I 244 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7197 (ttt90) REVERT: J 227 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8622 (ttpp) outliers start: 59 outliers final: 20 residues processed: 352 average time/residue: 1.6725 time to fit residues: 644.2277 Evaluate side-chains 329 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 302 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 0.0870 chunk 124 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN E 173 GLN F 121 ASN G 85 GLN G 121 ASN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN J 173 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19090 Z= 0.316 Angle : 0.577 8.189 25840 Z= 0.283 Chirality : 0.043 0.126 3030 Planarity : 0.004 0.035 3260 Dihedral : 4.545 13.673 2470 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.52 % Allowed : 19.68 % Favored : 77.80 % 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: 0.57 (0.18), residues: 2260 helix: 0.44 (0.20), residues: 640 sheet: 0.85 (0.18), residues: 820 loop : 0.01 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 186 HIS 0.003 0.001 HIS I 152 PHE 0.008 0.001 PHE C 71 TYR 0.010 0.002 TYR G 202 ARG 0.007 0.001 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 308 time to evaluate : 2.122 Fit side-chains REVERT: A 166 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7751 (ttm) REVERT: A 193 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: C 42 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7865 (mm) REVERT: C 227 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8488 (ttpp) REVERT: D 227 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8588 (ttpp) REVERT: E 42 LEU cc_start: 0.8327 (mm) cc_final: 0.8022 (mm) REVERT: E 227 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8633 (ttpp) REVERT: F 166 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7720 (ttm) REVERT: H 42 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7946 (mm) REVERT: H 148 GLU cc_start: 0.7749 (pt0) cc_final: 0.7386 (pt0) REVERT: H 227 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8545 (ttpp) REVERT: I 244 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (ttt90) REVERT: J 227 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8645 (ttpp) outliers start: 55 outliers final: 22 residues processed: 344 average time/residue: 1.6247 time to fit residues: 611.9566 Evaluate side-chains 318 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 285 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 240 MET Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 240 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 0.0970 chunk 132 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN E 173 GLN G 85 GLN G 121 ASN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN J 173 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19090 Z= 0.197 Angle : 0.532 8.372 25840 Z= 0.260 Chirality : 0.041 0.124 3030 Planarity : 0.003 0.032 3260 Dihedral : 4.269 13.827 2470 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 20.32 % Favored : 77.52 % 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: 0.59 (0.18), residues: 2260 helix: 0.66 (0.20), residues: 640 sheet: 0.68 (0.17), residues: 910 loop : -0.03 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 186 HIS 0.002 0.001 HIS J 119 PHE 0.006 0.001 PHE D 71 TYR 0.010 0.001 TYR F 103 ARG 0.006 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 305 time to evaluate : 2.593 Fit side-chains REVERT: B 166 MET cc_start: 0.8241 (ttm) cc_final: 0.7842 (ttm) REVERT: B 227 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8477 (ttpp) REVERT: C 42 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7807 (mm) REVERT: C 227 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8602 (ttmt) REVERT: D 104 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8601 (mmmt) REVERT: D 227 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8583 (ttpp) REVERT: E 42 LEU cc_start: 0.8269 (mm) cc_final: 0.7960 (mm) REVERT: E 227 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8618 (ttpp) REVERT: H 42 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7839 (mm) REVERT: H 148 GLU cc_start: 0.7719 (pt0) cc_final: 0.7390 (pt0) REVERT: H 193 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7185 (mp0) REVERT: H 227 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8533 (ttpp) REVERT: I 244 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7209 (ttt90) REVERT: J 227 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8616 (ttpp) outliers start: 47 outliers final: 24 residues processed: 333 average time/residue: 1.6070 time to fit residues: 586.5511 Evaluate side-chains 313 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 280 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 169 GLN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN E 173 GLN G 85 GLN G 121 ASN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19090 Z= 0.293 Angle : 0.573 8.336 25840 Z= 0.280 Chirality : 0.043 0.125 3030 Planarity : 0.004 0.050 3260 Dihedral : 4.501 14.899 2470 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.29 % Allowed : 20.55 % Favored : 77.16 % 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: 0.57 (0.18), residues: 2260 helix: 0.65 (0.20), residues: 640 sheet: 0.70 (0.17), residues: 910 loop : -0.09 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 186 HIS 0.004 0.001 HIS E 119 PHE 0.007 0.001 PHE C 71 TYR 0.013 0.001 TYR J 103 ARG 0.010 0.001 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 310 time to evaluate : 2.159 Fit side-chains REVERT: A 166 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7725 (ttm) REVERT: B 227 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8464 (ttpp) REVERT: C 42 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7790 (mm) REVERT: C 227 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8599 (ttmt) REVERT: D 227 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8586 (ttpp) REVERT: E 227 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8620 (ttpp) REVERT: F 166 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: H 42 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7848 (mm) REVERT: H 148 GLU cc_start: 0.7756 (pt0) cc_final: 0.7414 (pt0) REVERT: H 193 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7210 (mp0) REVERT: H 227 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8532 (ttpp) REVERT: I 244 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7231 (ttt90) REVERT: J 227 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8644 (ttpp) outliers start: 50 outliers final: 25 residues processed: 341 average time/residue: 1.7329 time to fit residues: 644.0115 Evaluate side-chains 341 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.4980 chunk 218 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 169 GLN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN E 173 GLN G 85 GLN G 121 ASN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.003 0.035 19090 Z= 0.208 Angle : 0.540 8.493 25840 Z= 0.264 Chirality : 0.042 0.124 3030 Planarity : 0.004 0.055 3260 Dihedral : 4.319 14.969 2470 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.93 % Allowed : 21.01 % Favored : 77.06 % 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: 0.66 (0.18), residues: 2260 helix: 0.75 (0.20), residues: 640 sheet: 0.72 (0.17), residues: 910 loop : -0.04 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 186 HIS 0.003 0.001 HIS E 119 PHE 0.006 0.001 PHE D 71 TYR 0.014 0.001 TYR E 103 ARG 0.011 0.001 ARG F 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 318 time to evaluate : 2.151 Fit side-chains REVERT: A 166 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7688 (ttm) REVERT: B 227 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8482 (ttpp) REVERT: C 42 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7800 (mm) REVERT: C 227 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8602 (ttmt) REVERT: E 227 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8623 (ttpp) REVERT: F 166 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: H 42 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7824 (mm) REVERT: H 148 GLU cc_start: 0.7712 (pt0) cc_final: 0.7376 (pt0) REVERT: H 193 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7195 (mp0) REVERT: H 227 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8535 (ttpp) REVERT: I 166 MET cc_start: 0.8114 (ttm) cc_final: 0.7880 (ttm) REVERT: I 244 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7239 (ttt90) REVERT: J 227 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8617 (ttpp) outliers start: 42 outliers final: 21 residues processed: 344 average time/residue: 1.6719 time to fit residues: 628.4597 Evaluate side-chains 330 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 299 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 187 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 169 GLN A 173 GLN B 85 GLN B 121 ASN B 173 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 121 ASN E 173 GLN G 85 GLN G 121 ASN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 85 GLN J 121 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106087 restraints weight = 19605.803| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.12 r_work: 0.2924 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19090 Z= 0.275 Angle : 0.574 8.359 25840 Z= 0.280 Chirality : 0.043 0.123 3030 Planarity : 0.004 0.062 3260 Dihedral : 4.496 15.100 2470 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.16 % Allowed : 20.87 % Favored : 76.97 % 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: 0.61 (0.18), residues: 2260 helix: 0.71 (0.20), residues: 640 sheet: 0.72 (0.17), residues: 910 loop : -0.10 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 186 HIS 0.003 0.001 HIS E 119 PHE 0.007 0.001 PHE D 71 TYR 0.015 0.002 TYR J 103 ARG 0.012 0.001 ARG F 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9649.31 seconds wall clock time: 170 minutes 46.00 seconds (10246.00 seconds total)