Starting phenix.real_space_refine on Fri Feb 16 18:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7b_28901/02_2024/8f7b_28901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7b_28901/02_2024/8f7b_28901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7b_28901/02_2024/8f7b_28901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7b_28901/02_2024/8f7b_28901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7b_28901/02_2024/8f7b_28901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7b_28901/02_2024/8f7b_28901_updated.pdb" } resolution = 3.15 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= 0.003 sd= 0.073 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 P 6 5.49 5 S 106 5.16 5 C 10678 2.51 5 N 2547 2.21 5 O 2829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D ASP 298": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 298": "OD1" <-> "OD2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 354": "OE1" <-> "OE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16166 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2672 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2668 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2654 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "D" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2648 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 102 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.51, per 1000 atoms: 0.53 Number of scatterers: 16166 At special positions: 0 Unit cell: (96.416, 106.896, 134.144, 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) S 106 16.00 P 6 15.00 O 2829 8.00 N 2547 7.00 C 10678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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=2.04 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 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " 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: 6.32 Conformation dependent library (CDL) restraints added in 2.6 seconds 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 6 sheets defined 68.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.188A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.966A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.581A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 288 removed outlier: 3.920A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.353A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 345 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.192A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 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 48 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 145 Proline residue: B 126 - end of helix removed outlier: 4.569A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 259 through 288 removed outlier: 4.810A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.544A pdb=" N CYS B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 4.315A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 23 through 49 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 4.619A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 234 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.842A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 344 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 394 removed outlier: 4.406A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 409 Processing helix chain 'D' and resid 23 through 49 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 145 Proline residue: D 126 - end of helix removed outlier: 4.602A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 254 Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.836A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 370 through 382 Processing helix chain 'D' and resid 384 through 394 removed outlier: 4.537A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 23 through 49 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 Proline residue: E 126 - end of helix removed outlier: 4.498A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 259 through 288 removed outlier: 4.914A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 344 removed outlier: 3.577A pdb=" N SER E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.566A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.900A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 408 Processing helix chain 'F' and resid 23 through 48 removed outlier: 3.689A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 118 Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 144 through 147 No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 149 through 167 Processing helix chain 'F' and resid 170 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 257 through 283 Processing helix chain 'F' and resid 311 through 342 removed outlier: 4.588A pdb=" N HIS F 314 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU F 315 " --> pdb=" O MET F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 355 No H-bonds generated for 'chain 'F' and resid 352 through 355' Processing helix chain 'F' and resid 369 through 380 Processing helix chain 'F' and resid 382 through 391 removed outlier: 4.895A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.601A pdb=" N VAL A 293 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= C, first strand: chain 'C' and resid 52 through 56 Processing sheet with id= D, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.636A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 52 through 56 980 hydrogen bonds defined for protein. 2766 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: 4.52 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4304 1.34 - 1.46: 3553 1.46 - 1.58: 8563 1.58 - 1.70: 7 1.70 - 1.82: 158 Bond restraints: 16585 Sorted by residual: bond pdb=" C10 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sigma weight residual 1.206 1.359 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.783 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" O4P PEE E 901 " pdb=" P PEE E 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" O4P PEE F 901 " pdb=" P PEE F 901 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 16580 not shown) Histogram of bond angle deviations from ideal: 90.60 - 99.33: 12 99.33 - 108.06: 619 108.06 - 116.79: 10319 116.79 - 125.52: 11117 125.52 - 134.25: 299 Bond angle restraints: 22366 Sorted by residual: angle pdb=" N LEU A 344 " pdb=" CA LEU A 344 " pdb=" C LEU A 344 " ideal model delta sigma weight residual 111.69 118.08 -6.39 1.23e+00 6.61e-01 2.70e+01 angle pdb=" O1P PEE F 901 " pdb=" P PEE F 901 " pdb=" O2P PEE F 901 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.23 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.21 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 22361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 9496 35.76 - 71.52: 307 71.52 - 107.28: 28 107.28 - 143.04: 8 143.04 - 178.80: 9 Dihedral angle restraints: 9848 sinusoidal: 4159 harmonic: 5689 Sorted by residual: dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 295 " pdb=" CB CYS A 295 " ideal model delta sinusoidal sigma weight residual 93.00 36.75 56.25 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" C4 PEE B 901 " pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " pdb=" O3P PEE B 901 " ideal model delta sinusoidal sigma weight residual 171.78 -7.02 178.80 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2260 0.082 - 0.164: 145 0.164 - 0.246: 9 0.246 - 0.328: 0 0.328 - 0.410: 2 Chirality restraints: 2416 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE E 53 " pdb=" CA ILE E 53 " pdb=" CG1 ILE E 53 " pdb=" CG2 ILE E 53 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2413 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.026 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP D 168 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 170 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP F 170 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 170 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 170 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 170 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 170 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 170 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 145 " -0.023 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP F 145 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 145 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 145 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 145 " 0.000 2.00e-02 2.50e+03 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3880 2.79 - 3.32: 15402 3.32 - 3.85: 28252 3.85 - 4.37: 32431 4.37 - 4.90: 55625 Nonbonded interactions: 135590 Sorted by model distance: nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR D 351 " pdb=" OD2 ASP D 380 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR A 316 " pdb=" OE2 GLU B 115 " model vdw 2.303 2.440 nonbonded pdb=" OD1 ASP F 50 " pdb=" NE2 HIS F 310 " model vdw 2.308 2.520 nonbonded pdb=" OD2 ASP F 50 " pdb=" OH TYR F 116 " model vdw 2.314 2.440 ... (remaining 135585 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 68 or resid 93 through 175 or resid 232 through \ 408 or resid 901 or (resid 902 and (name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 232 through \ 408 or (resid 901 and (name N or name C1 or 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 C18 or name C1 \ 9 or name C2 or name C20 or name C4 or name C5 or name O1P or name O2 or name O2 \ P or name O3P or name O4 or name O4P or name P )) or (resid 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or (resid 901 and (name N or name C1 or nam \ e C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C4 or name C5 o \ r name O1P or name O2 or name O2P or name O3P or name O4 or name O4P or name P ) \ ) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 232 through 408 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 232 through 408 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or (resid 902 and (name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.600 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.770 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 16585 Z= 0.332 Angle : 0.787 13.885 22366 Z= 0.423 Chirality : 0.044 0.410 2416 Planarity : 0.005 0.080 2701 Dihedral : 18.683 178.800 6113 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.23 % Allowed : 17.51 % Favored : 82.26 % 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: 1858 helix: 1.33 (0.13), residues: 1308 sheet: 0.62 (0.56), residues: 105 loop : -1.08 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 170 HIS 0.013 0.001 HIS C 155 PHE 0.044 0.002 PHE D 390 TYR 0.024 0.001 TYR C 284 ARG 0.012 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 265 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 MET cc_start: 0.7380 (tpt) cc_final: 0.7070 (tpt) REVERT: B 359 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 143 TRP cc_start: 0.7822 (t60) cc_final: 0.7459 (t60) REVERT: C 308 TYR cc_start: 0.9028 (m-80) cc_final: 0.8543 (m-80) REVERT: C 364 ASP cc_start: 0.5105 (p0) cc_final: 0.4800 (t0) REVERT: D 168 TRP cc_start: 0.6694 (t-100) cc_final: 0.6429 (t-100) REVERT: E 308 TYR cc_start: 0.9135 (m-80) cc_final: 0.8907 (m-80) REVERT: E 393 PHE cc_start: 0.7082 (m-80) cc_final: 0.6332 (m-80) REVERT: F 348 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6297 (tm-30) REVERT: F 387 ARG cc_start: 0.6728 (tmm160) cc_final: 0.6234 (tmm160) REVERT: F 392 LEU cc_start: 0.8295 (tp) cc_final: 0.8005 (tp) outliers start: 4 outliers final: 3 residues processed: 269 average time/residue: 0.2838 time to fit residues: 113.1838 Evaluate side-chains 249 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 246 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN C 46 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16585 Z= 0.174 Angle : 0.432 6.119 22366 Z= 0.237 Chirality : 0.036 0.122 2416 Planarity : 0.004 0.028 2701 Dihedral : 12.612 178.070 2319 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.65 % Allowed : 17.00 % Favored : 81.35 % 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: 1.96 (0.19), residues: 1858 helix: 2.04 (0.14), residues: 1324 sheet: 0.50 (0.54), residues: 105 loop : -0.84 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 145 HIS 0.011 0.001 HIS A 253 PHE 0.012 0.001 PHE F 158 TYR 0.013 0.001 TYR C 338 ARG 0.005 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7612 (t) cc_final: 0.6937 (p) REVERT: B 359 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6880 (mm-30) REVERT: C 143 TRP cc_start: 0.7880 (t60) cc_final: 0.7494 (t60) REVERT: C 364 ASP cc_start: 0.5096 (p0) cc_final: 0.4851 (p0) REVERT: D 168 TRP cc_start: 0.6904 (t-100) cc_final: 0.6652 (t-100) REVERT: E 393 PHE cc_start: 0.7361 (m-80) cc_final: 0.6679 (m-80) REVERT: F 300 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7380 (mtt) REVERT: F 392 LEU cc_start: 0.8198 (tp) cc_final: 0.7932 (tp) outliers start: 29 outliers final: 15 residues processed: 275 average time/residue: 0.2707 time to fit residues: 111.0846 Evaluate side-chains 252 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN B 267 GLN C 46 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN E 370 ASN F 107 GLN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 16585 Z= 0.568 Angle : 0.633 7.018 22366 Z= 0.342 Chirality : 0.045 0.178 2416 Planarity : 0.004 0.036 2701 Dihedral : 11.059 165.285 2315 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.98 % Allowed : 17.51 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 1858 helix: 1.53 (0.14), residues: 1324 sheet: 0.14 (0.53), residues: 105 loop : -1.15 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 170 HIS 0.011 0.002 HIS A 253 PHE 0.021 0.002 PHE A 374 TYR 0.023 0.002 TYR A 30 ARG 0.006 0.001 ARG F 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 228 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7537 (t) cc_final: 0.6887 (p) REVERT: A 104 HIS cc_start: 0.9110 (OUTLIER) cc_final: 0.8245 (m90) REVERT: A 265 MET cc_start: 0.8523 (tpt) cc_final: 0.8171 (tpt) REVERT: A 343 MET cc_start: 0.8992 (mtp) cc_final: 0.8640 (mtp) REVERT: B 403 ARG cc_start: 0.8477 (ttm110) cc_final: 0.8044 (ttm110) REVERT: C 364 ASP cc_start: 0.5230 (p0) cc_final: 0.4911 (p0) REVERT: D 104 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8734 (t70) REVERT: D 164 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: D 168 TRP cc_start: 0.7101 (t-100) cc_final: 0.6714 (t60) REVERT: D 249 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7860 (tptt) REVERT: D 287 HIS cc_start: 0.7961 (p90) cc_final: 0.7759 (p90) REVERT: E 309 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7800 (ttt180) REVERT: F 145 TRP cc_start: 0.6534 (p-90) cc_final: 0.6282 (p-90) REVERT: F 146 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: F 300 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7761 (mtp) REVERT: F 376 MET cc_start: 0.6671 (mmm) cc_final: 0.6466 (mmm) REVERT: F 392 LEU cc_start: 0.8294 (tp) cc_final: 0.7895 (tp) outliers start: 70 outliers final: 38 residues processed: 278 average time/residue: 0.2794 time to fit residues: 114.8147 Evaluate side-chains 261 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 406 ASN C 46 GLN C 49 GLN C 155 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN D 312 HIS F 46 GLN F 107 GLN F 134 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16585 Z= 0.177 Angle : 0.427 6.099 22366 Z= 0.236 Chirality : 0.037 0.136 2416 Planarity : 0.003 0.030 2701 Dihedral : 8.453 122.169 2315 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.39 % Allowed : 19.95 % Favored : 77.66 % 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: 1.81 (0.20), residues: 1858 helix: 1.94 (0.14), residues: 1319 sheet: 0.26 (0.52), residues: 105 loop : -0.87 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 170 HIS 0.010 0.001 HIS A 253 PHE 0.012 0.001 PHE E 324 TYR 0.014 0.001 TYR D 382 ARG 0.007 0.000 ARG F 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7618 (t) cc_final: 0.6952 (p) REVERT: C 104 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.8480 (t70) REVERT: C 245 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6801 (mp0) REVERT: C 364 ASP cc_start: 0.5337 (p0) cc_final: 0.5017 (p0) REVERT: D 386 TYR cc_start: 0.7841 (m-80) cc_final: 0.7546 (m-80) REVERT: E 309 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7739 (ttt180) REVERT: F 146 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: F 300 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7697 (mtp) REVERT: F 391 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: F 392 LEU cc_start: 0.8359 (tp) cc_final: 0.7941 (tp) outliers start: 42 outliers final: 19 residues processed: 278 average time/residue: 0.2898 time to fit residues: 119.2857 Evaluate side-chains 245 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN E 370 ASN E 377 HIS F 107 GLN F 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16585 Z= 0.340 Angle : 0.505 8.155 22366 Z= 0.273 Chirality : 0.040 0.134 2416 Planarity : 0.004 0.035 2701 Dihedral : 7.959 83.950 2313 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.84 % Allowed : 20.01 % Favored : 77.15 % 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: 1.64 (0.20), residues: 1858 helix: 1.84 (0.14), residues: 1319 sheet: -0.08 (0.53), residues: 106 loop : -0.94 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 145 HIS 0.015 0.001 HIS C 155 PHE 0.015 0.002 PHE A 374 TYR 0.014 0.002 TYR A 30 ARG 0.006 0.000 ARG F 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7597 (t) cc_final: 0.6915 (p) REVERT: B 17 TYR cc_start: 0.9000 (m-10) cc_final: 0.8618 (m-10) REVERT: B 243 LEU cc_start: 0.7823 (tt) cc_final: 0.7560 (tt) REVERT: B 403 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7826 (ptp-110) REVERT: C 245 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6882 (mp0) REVERT: C 364 ASP cc_start: 0.5249 (p0) cc_final: 0.4939 (p0) REVERT: C 380 ASP cc_start: 0.7762 (m-30) cc_final: 0.7457 (m-30) REVERT: D 164 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: E 309 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7789 (ttt180) REVERT: F 146 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: F 300 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7777 (mtp) REVERT: F 392 LEU cc_start: 0.8443 (tp) cc_final: 0.8076 (tp) outliers start: 50 outliers final: 35 residues processed: 266 average time/residue: 0.2758 time to fit residues: 109.9379 Evaluate side-chains 265 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 227 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN F 112 ASN F 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16585 Z= 0.229 Angle : 0.450 7.179 22366 Z= 0.245 Chirality : 0.037 0.124 2416 Planarity : 0.003 0.032 2701 Dihedral : 7.255 84.290 2313 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.90 % Allowed : 20.07 % Favored : 77.03 % 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: 1.80 (0.20), residues: 1858 helix: 1.95 (0.14), residues: 1317 sheet: 0.03 (0.54), residues: 100 loop : -0.83 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 145 HIS 0.012 0.001 HIS C 155 PHE 0.014 0.001 PHE D 250 TYR 0.015 0.001 TYR D 382 ARG 0.008 0.000 ARG F 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7563 (t) cc_final: 0.6905 (p) REVERT: B 17 TYR cc_start: 0.8953 (m-10) cc_final: 0.8568 (m-10) REVERT: B 168 TRP cc_start: 0.7807 (t-100) cc_final: 0.7475 (t-100) REVERT: B 171 ARG cc_start: 0.8455 (tpp80) cc_final: 0.8246 (tpp-160) REVERT: B 243 LEU cc_start: 0.7828 (tt) cc_final: 0.7570 (tt) REVERT: B 403 ARG cc_start: 0.8450 (ttm110) cc_final: 0.7919 (ptp90) REVERT: C 104 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8503 (t70) REVERT: C 245 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6894 (mp0) REVERT: C 364 ASP cc_start: 0.5300 (p0) cc_final: 0.4961 (p0) REVERT: C 380 ASP cc_start: 0.7700 (m-30) cc_final: 0.7358 (m-30) REVERT: D 164 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: D 168 TRP cc_start: 0.6685 (t60) cc_final: 0.5890 (t-100) REVERT: E 309 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7745 (ttt180) REVERT: F 50 ASP cc_start: 0.7676 (t0) cc_final: 0.7366 (t70) REVERT: F 145 TRP cc_start: 0.6566 (p-90) cc_final: 0.6232 (p-90) REVERT: F 146 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: F 300 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7741 (mtp) outliers start: 51 outliers final: 37 residues processed: 267 average time/residue: 0.2737 time to fit residues: 109.8716 Evaluate side-chains 263 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN F 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16585 Z= 0.182 Angle : 0.436 7.005 22366 Z= 0.236 Chirality : 0.037 0.130 2416 Planarity : 0.003 0.032 2701 Dihedral : 6.620 88.605 2313 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.79 % Allowed : 20.13 % Favored : 77.09 % 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: 1.99 (0.20), residues: 1858 helix: 2.07 (0.14), residues: 1320 sheet: 0.28 (0.55), residues: 99 loop : -0.76 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 170 HIS 0.012 0.001 HIS A 253 PHE 0.015 0.001 PHE D 250 TYR 0.013 0.001 TYR F 279 ARG 0.007 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 236 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7490 (t) cc_final: 0.6808 (p) REVERT: B 168 TRP cc_start: 0.7763 (t-100) cc_final: 0.7405 (t-100) REVERT: B 243 LEU cc_start: 0.7848 (tt) cc_final: 0.7577 (tt) REVERT: C 104 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8457 (t70) REVERT: C 245 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6821 (mp0) REVERT: C 364 ASP cc_start: 0.5387 (p0) cc_final: 0.5091 (p0) REVERT: C 380 ASP cc_start: 0.7541 (m-30) cc_final: 0.7132 (m-30) REVERT: D 164 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: E 309 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7723 (ttt180) REVERT: F 50 ASP cc_start: 0.7619 (t0) cc_final: 0.7299 (t70) REVERT: F 145 TRP cc_start: 0.6556 (p-90) cc_final: 0.6181 (p-90) REVERT: F 146 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: F 300 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7791 (mtp) outliers start: 49 outliers final: 36 residues processed: 275 average time/residue: 0.2667 time to fit residues: 111.7089 Evaluate side-chains 267 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 162 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 66 ASN A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16585 Z= 0.180 Angle : 0.436 7.819 22366 Z= 0.238 Chirality : 0.037 0.126 2416 Planarity : 0.003 0.032 2701 Dihedral : 6.346 84.787 2313 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.79 % Allowed : 20.75 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1858 helix: 2.14 (0.14), residues: 1320 sheet: 0.34 (0.54), residues: 99 loop : -0.74 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 170 HIS 0.017 0.001 HIS A 253 PHE 0.017 0.001 PHE D 144 TYR 0.013 0.001 TYR F 279 ARG 0.008 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7538 (t) cc_final: 0.6871 (p) REVERT: A 243 LEU cc_start: 0.8221 (mm) cc_final: 0.7986 (mt) REVERT: B 168 TRP cc_start: 0.7774 (t-100) cc_final: 0.7420 (t-100) REVERT: B 243 LEU cc_start: 0.7782 (tt) cc_final: 0.7509 (tt) REVERT: B 403 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7516 (ptp-170) REVERT: C 104 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8460 (t70) REVERT: C 143 TRP cc_start: 0.7904 (t60) cc_final: 0.7694 (t60) REVERT: C 245 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6815 (mp0) REVERT: C 364 ASP cc_start: 0.5382 (p0) cc_final: 0.5091 (p0) REVERT: C 380 ASP cc_start: 0.7563 (m-30) cc_final: 0.7160 (m-30) REVERT: D 164 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: D 168 TRP cc_start: 0.6699 (t60) cc_final: 0.5903 (t-100) REVERT: E 309 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7745 (ttt180) REVERT: F 145 TRP cc_start: 0.6475 (p-90) cc_final: 0.6066 (p-90) REVERT: F 146 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: F 300 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7794 (mtp) REVERT: F 348 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6394 (tm-30) outliers start: 49 outliers final: 37 residues processed: 270 average time/residue: 0.2684 time to fit residues: 109.1976 Evaluate side-chains 268 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 227 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16585 Z= 0.198 Angle : 0.448 7.870 22366 Z= 0.242 Chirality : 0.037 0.126 2416 Planarity : 0.003 0.032 2701 Dihedral : 6.229 78.196 2313 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.62 % Allowed : 21.26 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1858 helix: 2.11 (0.14), residues: 1325 sheet: 0.26 (0.53), residues: 105 loop : -0.81 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 170 HIS 0.015 0.001 HIS A 253 PHE 0.012 0.001 PHE D 250 TYR 0.013 0.001 TYR F 279 ARG 0.007 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7422 (t) cc_final: 0.6809 (p) REVERT: A 337 MET cc_start: 0.8653 (mmm) cc_final: 0.8135 (mmm) REVERT: B 168 TRP cc_start: 0.7792 (t-100) cc_final: 0.7445 (t-100) REVERT: B 243 LEU cc_start: 0.7779 (tt) cc_final: 0.7511 (tt) REVERT: B 403 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7536 (ptp-170) REVERT: C 104 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8517 (t70) REVERT: C 245 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6818 (mp0) REVERT: C 364 ASP cc_start: 0.5387 (p0) cc_final: 0.5104 (p0) REVERT: C 380 ASP cc_start: 0.7591 (m-30) cc_final: 0.7205 (m-30) REVERT: D 164 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: D 168 TRP cc_start: 0.6720 (t60) cc_final: 0.5911 (t-100) REVERT: E 309 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7754 (ttt180) REVERT: F 50 ASP cc_start: 0.7778 (t0) cc_final: 0.7493 (t70) REVERT: F 145 TRP cc_start: 0.6422 (p-90) cc_final: 0.5991 (p-90) REVERT: F 146 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: F 300 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: F 348 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6403 (tm-30) outliers start: 46 outliers final: 41 residues processed: 271 average time/residue: 0.2779 time to fit residues: 113.1345 Evaluate side-chains 273 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 146 optimal weight: 0.0040 chunk 15 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 0.0170 chunk 116 optimal weight: 0.6980 overall best weight: 0.3830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS C 404 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16585 Z= 0.136 Angle : 0.430 7.793 22366 Z= 0.231 Chirality : 0.036 0.127 2416 Planarity : 0.003 0.030 2701 Dihedral : 5.846 70.689 2313 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.22 % Allowed : 21.89 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.20), residues: 1858 helix: 2.22 (0.14), residues: 1324 sheet: 0.44 (0.52), residues: 105 loop : -0.77 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 170 HIS 0.012 0.001 HIS A 253 PHE 0.019 0.001 PHE D 144 TYR 0.013 0.001 TYR F 279 ARG 0.007 0.000 ARG F 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7411 (t) cc_final: 0.6789 (p) REVERT: A 337 MET cc_start: 0.8588 (mmm) cc_final: 0.8075 (mmm) REVERT: B 168 TRP cc_start: 0.7732 (t-100) cc_final: 0.7383 (t-100) REVERT: B 243 LEU cc_start: 0.7700 (tt) cc_final: 0.7422 (tt) REVERT: C 104 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8445 (t70) REVERT: C 245 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6830 (mp0) REVERT: C 364 ASP cc_start: 0.5287 (p0) cc_final: 0.5028 (p0) REVERT: C 380 ASP cc_start: 0.7622 (m-30) cc_final: 0.7200 (m-30) REVERT: D 164 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: D 168 TRP cc_start: 0.6677 (t60) cc_final: 0.5873 (t-100) REVERT: E 309 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7734 (ttt-90) REVERT: F 145 TRP cc_start: 0.6444 (p-90) cc_final: 0.5981 (p-90) REVERT: F 146 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: F 251 HIS cc_start: 0.7110 (t-90) cc_final: 0.6873 (t-90) REVERT: F 300 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7797 (mtp) REVERT: F 348 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6426 (tm-30) outliers start: 39 outliers final: 30 residues processed: 272 average time/residue: 0.2760 time to fit residues: 112.6094 Evaluate side-chains 260 residues out of total 1759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 226 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN F 46 GLN F 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.166586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120384 restraints weight = 20580.205| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.31 r_work: 0.3380 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16585 Z= 0.177 Angle : 0.456 8.999 22366 Z= 0.244 Chirality : 0.037 0.140 2416 Planarity : 0.003 0.032 2701 Dihedral : 5.912 66.293 2313 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.27 % Allowed : 21.83 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1858 helix: 2.21 (0.14), residues: 1325 sheet: 0.31 (0.52), residues: 105 loop : -0.77 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 170 HIS 0.011 0.001 HIS A 253 PHE 0.017 0.001 PHE D 250 TYR 0.013 0.001 TYR F 279 ARG 0.007 0.000 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3713.60 seconds wall clock time: 68 minutes 14.93 seconds (4094.93 seconds total)