Starting phenix.real_space_refine on Mon Dec 11 00:23:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m17_23614/12_2023/7m17_23614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m17_23614/12_2023/7m17_23614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m17_23614/12_2023/7m17_23614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m17_23614/12_2023/7m17_23614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m17_23614/12_2023/7m17_23614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m17_23614/12_2023/7m17_23614_updated.pdb" } resolution = 3.65 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= 0.002 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: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10639 2.51 5 N 2532 2.21 5 O 2764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 389": "NH1" <-> "NH2" Residue "F GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16039 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'PEE': 3, 'YNJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.01, per 1000 atoms: 0.56 Number of scatterers: 16039 At special positions: 0 Unit cell: (112.563, 100.056, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " 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: 6.23 Conformation dependent library (CDL) restraints added in 2.8 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 6 sheets defined 67.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 120 through 145 removed outlier: 3.553A pdb=" N PHE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 4.485A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 4.711A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 4.137A pdb=" N LEU A 173 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 254 Processing helix chain 'A' and resid 259 through 288 removed outlier: 3.751A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.322A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.947A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 145 removed outlier: 5.100A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 4.569A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 259 through 288 removed outlier: 3.986A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 346 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 23 through 48 removed outlier: 4.319A pdb=" N PHE C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR C 28 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER C 32 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 3.584A pdb=" N LEU C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 removed outlier: 4.597A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 234 through 256 removed outlier: 3.597A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 288 removed outlier: 3.729A pdb=" N THR C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 345 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.691A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 23 through 48 removed outlier: 4.022A pdb=" N PHE D 27 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR D 28 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 32 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET D 35 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 47 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 125 through 145 removed outlier: 4.464A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.876A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 234 through 255 removed outlier: 3.610A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 288 removed outlier: 3.705A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 346 Processing helix chain 'D' and resid 354 through 360 removed outlier: 4.457A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 removed outlier: 3.757A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 27 through 48 Processing helix chain 'E' and resid 103 through 116 removed outlier: 3.616A pdb=" N VAL E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 145 removed outlier: 3.635A pdb=" N PHE E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.936A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 removed outlier: 4.684A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.667A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 288 removed outlier: 3.836A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 346 Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.668A pdb=" N ILE E 356 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 358 " --> pdb=" O SER E 355 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 360 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 382 removed outlier: 3.903A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 388 No H-bonds generated for 'chain 'E' and resid 385 through 388' Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 407 Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'F' and resid 23 through 48 removed outlier: 4.471A pdb=" N PHE F 27 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER F 32 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET F 35 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 47 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 116 Processing helix chain 'F' and resid 120 through 145 removed outlier: 3.645A pdb=" N PHE F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.438A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 164 removed outlier: 4.459A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 235 through 254 Processing helix chain 'F' and resid 259 through 288 removed outlier: 3.757A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASN F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 345 Processing helix chain 'F' and resid 354 through 360 removed outlier: 4.111A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 384 through 389 Processing helix chain 'F' and resid 396 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.856A pdb=" N CYS A 295 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.942A pdb=" N VAL B 293 " --> pdb=" O CYS B 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 52 through 56 removed outlier: 3.518A pdb=" N ILE C 53 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 293 " --> pdb=" O CYS C 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.548A pdb=" N ILE D 53 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.502A pdb=" N CYS E 295 " --> pdb=" O TYR E 308 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 53 through 56 882 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2379 1.31 - 1.44: 4937 1.44 - 1.57: 9003 1.57 - 1.70: 8 1.70 - 1.82: 146 Bond restraints: 16473 Sorted by residual: bond pdb=" C18 PEE D 902 " pdb=" C19 PEE D 902 " ideal model delta sigma weight residual 1.523 1.339 0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C18 PEE A 901 " pdb=" C19 PEE A 901 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C18 PEE C 903 " pdb=" C19 PEE C 903 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C18 PEE E 902 " pdb=" C19 PEE E 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C18 PEE F 902 " pdb=" C19 PEE F 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.34e+01 ... (remaining 16468 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.36: 199 104.36 - 111.95: 7439 111.95 - 119.54: 6151 119.54 - 127.14: 8229 127.14 - 134.73: 204 Bond angle restraints: 22222 Sorted by residual: angle pdb=" CA PRO E 15 " pdb=" N PRO E 15 " pdb=" CD PRO E 15 " ideal model delta sigma weight residual 112.00 102.61 9.39 1.40e+00 5.10e-01 4.50e+01 angle pdb=" C THR A 48 " pdb=" N GLN A 49 " pdb=" CA GLN A 49 " ideal model delta sigma weight residual 121.90 114.40 7.50 1.26e+00 6.30e-01 3.54e+01 angle pdb=" CA PRO F 366 " pdb=" N PRO F 366 " pdb=" CD PRO F 366 " ideal model delta sigma weight residual 112.00 104.11 7.89 1.40e+00 5.10e-01 3.18e+01 angle pdb=" C THR D 48 " pdb=" N GLN D 49 " pdb=" CA GLN D 49 " ideal model delta sigma weight residual 121.90 114.91 6.99 1.26e+00 6.30e-01 3.08e+01 angle pdb=" C CYS C 280 " pdb=" N TYR C 281 " pdb=" CA TYR C 281 " ideal model delta sigma weight residual 122.09 113.63 8.46 1.79e+00 3.12e-01 2.23e+01 ... (remaining 22217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 9200 27.09 - 54.19: 532 54.19 - 81.28: 26 81.28 - 108.37: 10 108.37 - 135.47: 6 Dihedral angle restraints: 9774 sinusoidal: 4122 harmonic: 5652 Sorted by residual: dihedral pdb=" CA GLN A 105 " pdb=" C GLN A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR F 264 " pdb=" C TYR F 264 " pdb=" N MET F 265 " pdb=" CA MET F 265 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA TYR E 264 " pdb=" C TYR E 264 " pdb=" N MET E 265 " pdb=" CA MET E 265 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1915 0.062 - 0.124: 441 0.124 - 0.187: 47 0.187 - 0.249: 4 0.249 - 0.311: 1 Chirality restraints: 2408 Sorted by residual: chirality pdb=" C05 YNJ C 902 " pdb=" C06 YNJ C 902 " pdb=" C13 YNJ C 902 " pdb=" C27 YNJ C 902 " both_signs ideal model delta sigma weight residual False 3.00 2.69 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE C 365 " pdb=" CA ILE C 365 " pdb=" CG1 ILE C 365 " pdb=" CG2 ILE C 365 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO F 366 " pdb=" N PRO F 366 " pdb=" C PRO F 366 " pdb=" CB PRO F 366 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2405 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 325 " 0.012 2.00e-02 2.50e+03 1.86e-02 6.93e+00 pdb=" CG TYR A 325 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 325 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 325 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 325 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 325 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 325 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 325 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 275 " -0.013 2.00e-02 2.50e+03 1.87e-02 6.10e+00 pdb=" CG PHE A 275 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 275 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 275 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 275 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 275 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 275 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 143 " -0.019 2.00e-02 2.50e+03 1.54e-02 5.95e+00 pdb=" CG TRP B 143 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 143 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 143 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 143 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 143 " 0.000 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2830 2.77 - 3.30: 15046 3.30 - 3.83: 26566 3.83 - 4.37: 28662 4.37 - 4.90: 50362 Nonbonded interactions: 123466 Sorted by model distance: nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 48 " model vdw 2.234 2.440 nonbonded pdb=" OD2 ASP F 50 " pdb=" OH TYR F 114 " model vdw 2.237 2.440 nonbonded pdb=" OD2 ASP D 50 " pdb=" OH TYR D 114 " model vdw 2.252 2.440 nonbonded pdb=" O SER D 395 " pdb=" OG SER D 398 " model vdw 2.256 2.440 nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.257 2.440 ... (remaining 123461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 408 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or resid 903)) selection = (chain 'B' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'F' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 10.690 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 45.310 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.010 0.184 16473 Z= 0.607 Angle : 1.024 14.123 22222 Z= 0.503 Chirality : 0.052 0.311 2408 Planarity : 0.005 0.050 2673 Dihedral : 15.768 135.465 6060 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.06 (0.19), residues: 1842 helix: -0.22 (0.14), residues: 1254 sheet: -0.33 (0.52), residues: 96 loop : -1.75 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 143 HIS 0.014 0.002 HIS A 377 PHE 0.042 0.002 PHE A 275 TYR 0.043 0.002 TYR A 325 ARG 0.002 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2297 time to fit residues: 88.7349 Evaluate side-chains 179 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 88 optimal weight: 0.0570 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 0.0060 overall best weight: 0.1630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 253 HIS B 155 HIS C 105 GLN C 155 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 105 GLN D 406 ASN E 105 GLN E 267 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 16473 Z= 0.135 Angle : 0.526 11.214 22222 Z= 0.281 Chirality : 0.039 0.154 2408 Planarity : 0.004 0.041 2673 Dihedral : 9.576 103.104 2298 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.37 % Allowed : 8.88 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1842 helix: 0.63 (0.15), residues: 1248 sheet: -0.65 (0.53), residues: 102 loop : -1.62 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 168 HIS 0.009 0.001 HIS A 253 PHE 0.015 0.001 PHE D 275 TYR 0.031 0.001 TYR C 281 ARG 0.002 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 257 average time/residue: 0.2383 time to fit residues: 96.4874 Evaluate side-chains 207 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1410 time to fit residues: 6.0131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 182 optimal weight: 0.0270 chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 288 ASN C 155 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16473 Z= 0.238 Angle : 0.565 9.263 22222 Z= 0.300 Chirality : 0.040 0.128 2408 Planarity : 0.003 0.042 2673 Dihedral : 8.046 67.027 2298 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.78 % Allowed : 13.00 % Favored : 85.22 % 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: 0.51 (0.20), residues: 1842 helix: 1.03 (0.15), residues: 1218 sheet: 0.11 (0.52), residues: 96 loop : -1.15 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 168 HIS 0.009 0.001 HIS C 155 PHE 0.020 0.001 PHE E 144 TYR 0.028 0.001 TYR F 325 ARG 0.002 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 214 average time/residue: 0.2292 time to fit residues: 79.1033 Evaluate side-chains 183 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1479 time to fit residues: 6.7671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN E 155 HIS ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16473 Z= 0.167 Angle : 0.529 10.911 22222 Z= 0.279 Chirality : 0.039 0.206 2408 Planarity : 0.003 0.040 2673 Dihedral : 7.412 59.904 2298 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.55 % Allowed : 14.66 % Favored : 83.79 % 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: 0.71 (0.20), residues: 1842 helix: 1.16 (0.15), residues: 1218 sheet: 0.37 (0.51), residues: 96 loop : -1.05 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 168 HIS 0.010 0.001 HIS D 132 PHE 0.012 0.001 PHE F 125 TYR 0.022 0.001 TYR E 325 ARG 0.001 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 210 average time/residue: 0.2404 time to fit residues: 79.8001 Evaluate side-chains 195 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1550 time to fit residues: 5.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16473 Z= 0.286 Angle : 0.588 10.958 22222 Z= 0.310 Chirality : 0.042 0.180 2408 Planarity : 0.003 0.041 2673 Dihedral : 7.342 59.694 2298 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.72 % Allowed : 16.84 % Favored : 81.44 % 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: 0.74 (0.20), residues: 1842 helix: 1.17 (0.16), residues: 1218 sheet: 0.49 (0.50), residues: 96 loop : -1.01 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 168 HIS 0.008 0.001 HIS B 155 PHE 0.014 0.001 PHE D 125 TYR 0.031 0.001 TYR F 325 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 203 average time/residue: 0.2364 time to fit residues: 76.4498 Evaluate side-chains 183 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1482 time to fit residues: 5.3524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16473 Z= 0.182 Angle : 0.539 10.862 22222 Z= 0.284 Chirality : 0.040 0.154 2408 Planarity : 0.003 0.039 2673 Dihedral : 6.985 57.818 2298 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.32 % Allowed : 18.67 % Favored : 80.01 % 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: 0.89 (0.21), residues: 1842 helix: 1.27 (0.16), residues: 1218 sheet: 0.70 (0.51), residues: 96 loop : -0.97 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 168 HIS 0.011 0.001 HIS B 155 PHE 0.013 0.001 PHE F 125 TYR 0.024 0.001 TYR F 325 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 204 average time/residue: 0.2511 time to fit residues: 80.6248 Evaluate side-chains 185 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1653 time to fit residues: 6.2217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 0.0060 chunk 109 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN C 132 HIS ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 288 ASN E 155 HIS ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16473 Z= 0.145 Angle : 0.523 11.721 22222 Z= 0.275 Chirality : 0.039 0.148 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.554 59.364 2298 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.03 % Allowed : 19.64 % Favored : 79.32 % 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: 0.98 (0.21), residues: 1842 helix: 1.35 (0.16), residues: 1218 sheet: 0.95 (0.51), residues: 96 loop : -0.99 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 168 HIS 0.011 0.001 HIS B 155 PHE 0.012 0.001 PHE F 125 TYR 0.025 0.001 TYR E 325 ARG 0.008 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 209 average time/residue: 0.2480 time to fit residues: 81.6194 Evaluate side-chains 184 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1488 time to fit residues: 3.6161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 312 HIS C 132 HIS ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 288 ASN ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16473 Z= 0.141 Angle : 0.529 11.450 22222 Z= 0.275 Chirality : 0.039 0.151 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.268 58.188 2298 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.15 % Allowed : 19.99 % Favored : 78.87 % 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: 0.92 (0.21), residues: 1842 helix: 1.31 (0.16), residues: 1230 sheet: 1.22 (0.51), residues: 96 loop : -1.17 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 168 HIS 0.012 0.001 HIS B 155 PHE 0.012 0.001 PHE F 125 TYR 0.027 0.001 TYR E 325 ARG 0.008 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 219 average time/residue: 0.2543 time to fit residues: 87.1082 Evaluate side-chains 197 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1970 time to fit residues: 5.9263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16473 Z= 0.156 Angle : 0.548 12.140 22222 Z= 0.284 Chirality : 0.039 0.161 2408 Planarity : 0.003 0.038 2673 Dihedral : 6.146 54.776 2298 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.63 % Allowed : 20.68 % Favored : 78.69 % 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: 0.92 (0.21), residues: 1842 helix: 1.29 (0.16), residues: 1230 sheet: 1.39 (0.51), residues: 96 loop : -1.17 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 168 HIS 0.013 0.001 HIS B 155 PHE 0.012 0.001 PHE F 125 TYR 0.027 0.001 TYR E 325 ARG 0.009 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 202 average time/residue: 0.2455 time to fit residues: 79.1468 Evaluate side-chains 186 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1580 time to fit residues: 3.3930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 253 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS F 267 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16473 Z= 0.193 Angle : 0.569 12.686 22222 Z= 0.294 Chirality : 0.040 0.177 2408 Planarity : 0.003 0.039 2673 Dihedral : 6.147 51.792 2298 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.57 % Allowed : 20.85 % Favored : 78.58 % 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 (0.21), residues: 1842 helix: 1.29 (0.16), residues: 1230 sheet: 1.44 (0.50), residues: 96 loop : -1.13 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 168 HIS 0.014 0.001 HIS B 155 PHE 0.013 0.001 PHE F 125 TYR 0.027 0.001 TYR E 325 ARG 0.009 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 194 average time/residue: 0.2445 time to fit residues: 75.2262 Evaluate side-chains 191 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1670 time to fit residues: 4.3801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS B 116 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.123912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093682 restraints weight = 37235.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095730 restraints weight = 17601.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097452 restraints weight = 10188.936| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16473 Z= 0.226 Angle : 0.600 14.957 22222 Z= 0.308 Chirality : 0.041 0.161 2408 Planarity : 0.003 0.047 2673 Dihedral : 6.217 50.706 2298 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.52 % Allowed : 20.62 % Favored : 78.87 % 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: 0.87 (0.21), residues: 1842 helix: 1.23 (0.16), residues: 1230 sheet: 1.41 (0.49), residues: 96 loop : -1.11 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 168 HIS 0.013 0.001 HIS B 155 PHE 0.013 0.001 PHE F 125 TYR 0.026 0.001 TYR E 325 ARG 0.011 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.34 seconds wall clock time: 52 minutes 34.70 seconds (3154.70 seconds total)