Starting phenix.real_space_refine on Fri Feb 16 17:46:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/02_2024/7m19_23616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/02_2024/7m19_23616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/02_2024/7m19_23616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/02_2024/7m19_23616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/02_2024/7m19_23616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/02_2024/7m19_23616_updated.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10639 2.51 5 N 2532 2.21 5 O 2764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 389": "NH1" <-> "NH2" 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: 16039 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'PEE': 3, 'YNJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 8.96, per 1000 atoms: 0.56 Number of scatterers: 16039 At special positions: 0 Unit cell: (110.289, 101.193, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 2.8 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 6 sheets defined 67.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 23 through 48 removed outlier: 3.562A pdb=" N VAL A 26 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE A 27 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A 28 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 120 through 145 removed outlier: 3.918A pdb=" N TYR A 124 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE A 125 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 3.726A pdb=" N PHE A 142 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP A 143 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 145 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.403A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.927A pdb=" N LEU A 173 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 259 through 288 removed outlier: 3.900A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.611A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.811A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 120 through 145 removed outlier: 4.282A pdb=" N TYR B 124 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE B 125 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 4.103A pdb=" N PHE B 142 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 145 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 4.462A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.568A pdb=" N THR B 170 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 254 Processing helix chain 'B' and resid 259 through 288 removed outlier: 3.959A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 346 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'C' and resid 23 through 48 removed outlier: 4.239A pdb=" N PHE C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR C 28 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C 32 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 4.770A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 removed outlier: 4.382A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.514A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 288 removed outlier: 3.998A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 346 Processing helix chain 'C' and resid 354 through 360 removed outlier: 4.703A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 384 through 394 removed outlier: 4.168A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'D' and resid 17 through 20 Processing helix chain 'D' and resid 23 through 48 removed outlier: 4.188A pdb=" N PHE D 27 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR D 28 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET D 35 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 47 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 145 removed outlier: 3.999A pdb=" N TYR D 124 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 4.468A pdb=" N PHE D 142 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP D 143 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 145 " --> pdb=" O PHE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 4.324A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 234 through 254 removed outlier: 3.501A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 288 removed outlier: 3.802A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 353 through 360 removed outlier: 4.996A pdb=" N GLU D 358 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 removed outlier: 3.649A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 17 through 20 Processing helix chain 'E' and resid 23 through 48 removed outlier: 4.238A pdb=" N PHE E 27 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR E 28 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 47 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 removed outlier: 4.177A pdb=" N TYR E 124 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE E 125 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.837A pdb=" N PHE E 142 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP E 143 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 145 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 removed outlier: 4.449A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.747A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 288 removed outlier: 3.726A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 345 Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.715A pdb=" N ARG E 357 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU E 358 " --> pdb=" O SER E 355 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 360 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 382 removed outlier: 3.892A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.552A pdb=" N PHE E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 407 Processing helix chain 'F' and resid 23 through 48 removed outlier: 4.396A pdb=" N PHE F 27 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET F 35 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 47 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 116 Processing helix chain 'F' and resid 120 through 145 removed outlier: 4.146A pdb=" N TYR F 124 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE F 125 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.100A pdb=" N PHE F 142 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP F 143 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 164 removed outlier: 4.071A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 235 through 254 Processing helix chain 'F' and resid 259 through 288 removed outlier: 3.524A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 345 Processing helix chain 'F' and resid 354 through 360 removed outlier: 3.916A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'F' and resid 396 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 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 53 through 56 Processing sheet with id= D, first strand: chain 'D' and resid 292 through 296 removed outlier: 3.891A pdb=" N VAL D 293 " --> pdb=" O CYS D 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.555A 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 removed outlier: 3.814A pdb=" N VAL F 293 " --> pdb=" O CYS F 310 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2091 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: 4.18 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2379 1.31 - 1.44: 4937 1.44 - 1.57: 9006 1.57 - 1.69: 5 1.69 - 1.82: 146 Bond restraints: 16473 Sorted by residual: bond pdb=" C18 PEE B 902 " pdb=" C19 PEE B 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" C18 PEE C 903 " pdb=" C19 PEE C 903 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE F 902 " pdb=" C19 PEE F 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE C 904 " pdb=" C19 PEE C 904 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C18 PEE E 902 " pdb=" C19 PEE E 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 16468 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.88: 243 105.88 - 112.97: 8485 112.97 - 120.05: 6514 120.05 - 127.14: 6773 127.14 - 134.23: 207 Bond angle restraints: 22222 Sorted by residual: angle pdb=" C THR E 48 " pdb=" N GLN E 49 " pdb=" CA GLN E 49 " ideal model delta sigma weight residual 121.90 114.34 7.56 1.26e+00 6.30e-01 3.60e+01 angle pdb=" N GLU E 154 " pdb=" CA GLU E 154 " pdb=" CB GLU E 154 " ideal model delta sigma weight residual 110.28 118.21 -7.93 1.55e+00 4.16e-01 2.62e+01 angle pdb=" C ASN F 370 " pdb=" N ASP F 371 " pdb=" CA ASP F 371 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLU F 245 " pdb=" N LYS F 246 " pdb=" CA LYS F 246 " ideal model delta sigma weight residual 120.68 113.66 7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" C CYS B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta sigma weight residual 122.36 115.31 7.05 1.72e+00 3.38e-01 1.68e+01 ... (remaining 22217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 9067 24.81 - 49.61: 640 49.61 - 74.42: 45 74.42 - 99.23: 14 99.23 - 124.03: 8 Dihedral angle restraints: 9774 sinusoidal: 4122 harmonic: 5652 Sorted by residual: dihedral pdb=" CA GLN A 105 " pdb=" C GLN A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER D 352 " pdb=" C SER D 352 " pdb=" N PHE D 353 " pdb=" CA PHE D 353 " ideal model delta harmonic sigma weight residual 180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C12 PEE B 902 " pdb=" C10 PEE B 902 " pdb=" C11 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sinusoidal sigma weight residual -19.47 104.56 -124.03 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1922 0.062 - 0.124: 434 0.124 - 0.186: 48 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 2408 Sorted by residual: chirality pdb=" CB VAL E 297 " pdb=" CA VAL E 297 " pdb=" CG1 VAL E 297 " pdb=" CG2 VAL E 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C05 YNJ C 902 " pdb=" C06 YNJ C 902 " pdb=" C13 YNJ C 902 " pdb=" C27 YNJ C 902 " both_signs ideal model delta sigma weight residual False 3.00 2.70 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE E 365 " pdb=" CA ILE E 365 " pdb=" CG1 ILE E 365 " pdb=" CG2 ILE E 365 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2405 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 275 " -0.018 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 275 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE D 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 275 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 275 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 275 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 244 " -0.018 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE E 244 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE E 244 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 244 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 244 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 244 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 244 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 136 " -0.020 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE C 136 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 136 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 136 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 136 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 136 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 136 " -0.003 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2747 2.77 - 3.30: 15285 3.30 - 3.83: 26576 3.83 - 4.37: 28814 4.37 - 4.90: 50255 Nonbonded interactions: 123677 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.231 2.440 nonbonded pdb=" O THR D 44 " pdb=" OG1 THR D 48 " model vdw 2.267 2.440 nonbonded pdb=" OD2 ASP E 50 " pdb=" OH TYR E 114 " model vdw 2.269 2.440 nonbonded pdb=" OD2 ASP C 50 " pdb=" OH TYR C 114 " model vdw 2.273 2.440 nonbonded pdb=" O SER D 395 " pdb=" OG SER D 398 " model vdw 2.273 2.440 ... (remaining 123672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 408 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or resid 903)) selection = (chain 'B' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'F' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 10.570 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 43.010 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.009 0.183 16473 Z= 0.594 Angle : 1.031 12.279 22222 Z= 0.508 Chirality : 0.052 0.310 2408 Planarity : 0.005 0.042 2673 Dihedral : 15.738 124.033 6060 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.26 % 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: -0.78 (0.19), residues: 1842 helix: 0.04 (0.14), residues: 1236 sheet: 0.66 (0.49), residues: 96 loop : -1.95 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 143 HIS 0.019 0.002 HIS E 377 PHE 0.057 0.002 PHE D 275 TYR 0.022 0.002 TYR A 332 ARG 0.007 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8215 (tmt-80) cc_final: 0.7964 (tpt170) REVERT: B 325 TYR cc_start: 0.8747 (t80) cc_final: 0.8428 (t80) REVERT: C 336 CYS cc_start: 0.8318 (m) cc_final: 0.8114 (t) REVERT: D 37 MET cc_start: 0.8513 (ptp) cc_final: 0.8311 (ptt) REVERT: D 351 TYR cc_start: 0.6384 (t80) cc_final: 0.5922 (t80) REVERT: D 399 GLU cc_start: 0.8353 (mp0) cc_final: 0.7554 (mp0) REVERT: E 162 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8758 (mmtm) REVERT: F 249 LYS cc_start: 0.9154 (tptt) cc_final: 0.8574 (pttt) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.2611 time to fit residues: 101.4830 Evaluate side-chains 187 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 155 HIS A 288 ASN B 253 HIS B 288 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS E 116 ASN E 155 HIS F 381 GLN F 400 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16473 Z= 0.249 Angle : 0.591 11.579 22222 Z= 0.328 Chirality : 0.041 0.129 2408 Planarity : 0.005 0.032 2673 Dihedral : 9.414 79.719 2298 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.72 % Allowed : 10.42 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1842 helix: 0.50 (0.15), residues: 1218 sheet: 0.90 (0.49), residues: 96 loop : -1.70 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 143 HIS 0.007 0.001 HIS D 377 PHE 0.019 0.001 PHE C 136 TYR 0.018 0.001 TYR D 332 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8439 (tmt-80) cc_final: 0.8214 (tpt170) REVERT: A 288 ASN cc_start: 0.9366 (OUTLIER) cc_final: 0.9080 (t0) REVERT: B 325 TYR cc_start: 0.8853 (t80) cc_final: 0.8555 (t80) REVERT: C 161 LEU cc_start: 0.8790 (mm) cc_final: 0.8484 (mm) REVERT: E 162 LYS cc_start: 0.8971 (ttmm) cc_final: 0.8746 (mmtm) REVERT: E 386 TYR cc_start: 0.8256 (m-80) cc_final: 0.7958 (m-80) REVERT: F 154 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8413 (mm-30) REVERT: F 249 LYS cc_start: 0.9183 (tptt) cc_final: 0.8613 (pttt) outliers start: 30 outliers final: 16 residues processed: 211 average time/residue: 0.2617 time to fit residues: 84.8195 Evaluate side-chains 179 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 381 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16473 Z= 0.151 Angle : 0.523 11.493 22222 Z= 0.285 Chirality : 0.039 0.116 2408 Planarity : 0.004 0.036 2673 Dihedral : 7.638 67.923 2298 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.00 % Allowed : 14.32 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1842 helix: 0.83 (0.16), residues: 1188 sheet: 1.34 (0.50), residues: 96 loop : -1.38 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 143 HIS 0.009 0.001 HIS B 253 PHE 0.018 0.001 PHE C 136 TYR 0.013 0.001 TYR E 351 ARG 0.002 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8552 (mtt) cc_final: 0.8174 (tmm) REVERT: A 359 GLU cc_start: 0.7101 (pm20) cc_final: 0.6716 (tm-30) REVERT: B 288 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8636 (t0) REVERT: B 325 TYR cc_start: 0.8769 (t80) cc_final: 0.8440 (t80) REVERT: C 48 THR cc_start: 0.8424 (m) cc_final: 0.8073 (p) REVERT: C 161 LEU cc_start: 0.8780 (mm) cc_final: 0.8454 (mm) REVERT: D 280 CYS cc_start: 0.8697 (m) cc_final: 0.8398 (m) REVERT: E 162 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8715 (mmtm) REVERT: E 168 TRP cc_start: 0.7270 (t60) cc_final: 0.6705 (t60) REVERT: F 154 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8377 (mm-30) REVERT: F 245 GLU cc_start: 0.8640 (mp0) cc_final: 0.8213 (mm-30) REVERT: F 249 LYS cc_start: 0.9184 (tptt) cc_final: 0.8638 (pttt) REVERT: F 289 ILE cc_start: 0.9003 (pt) cc_final: 0.8761 (mt) REVERT: F 381 GLN cc_start: 0.8405 (tp40) cc_final: 0.8012 (mm-40) outliers start: 35 outliers final: 20 residues processed: 227 average time/residue: 0.2547 time to fit residues: 88.7216 Evaluate side-chains 209 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.0670 chunk 169 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 160 optimal weight: 0.0170 chunk 48 optimal weight: 0.9980 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16473 Z= 0.148 Angle : 0.497 8.123 22222 Z= 0.272 Chirality : 0.039 0.213 2408 Planarity : 0.004 0.031 2673 Dihedral : 7.068 63.485 2298 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.63 % Allowed : 16.72 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1842 helix: 0.86 (0.16), residues: 1206 sheet: 1.48 (0.51), residues: 96 loop : -1.58 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 143 HIS 0.009 0.001 HIS B 253 PHE 0.028 0.001 PHE C 250 TYR 0.012 0.001 TYR A 332 ARG 0.001 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 ASN cc_start: 0.9266 (t0) cc_final: 0.8392 (t0) REVERT: A 337 MET cc_start: 0.8558 (mtt) cc_final: 0.8195 (tmm) REVERT: A 359 GLU cc_start: 0.7147 (pm20) cc_final: 0.6802 (tm-30) REVERT: B 325 TYR cc_start: 0.8736 (t80) cc_final: 0.8411 (t80) REVERT: C 161 LEU cc_start: 0.8786 (mm) cc_final: 0.8484 (mm) REVERT: D 161 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7693 (pp) REVERT: E 162 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8773 (mmtm) REVERT: E 348 LEU cc_start: 0.8730 (tp) cc_final: 0.8474 (tp) REVERT: E 379 ILE cc_start: 0.8254 (tp) cc_final: 0.8024 (tp) REVERT: F 154 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8368 (mm-30) REVERT: F 249 LYS cc_start: 0.9189 (tptt) cc_final: 0.8642 (pttt) outliers start: 46 outliers final: 32 residues processed: 243 average time/residue: 0.2608 time to fit residues: 96.5736 Evaluate side-chains 221 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 153 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16473 Z= 0.153 Angle : 0.505 10.480 22222 Z= 0.274 Chirality : 0.038 0.184 2408 Planarity : 0.004 0.029 2673 Dihedral : 6.834 62.392 2298 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.55 % Allowed : 17.12 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1842 helix: 0.93 (0.16), residues: 1206 sheet: 1.58 (0.50), residues: 96 loop : -1.53 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 143 HIS 0.010 0.001 HIS B 253 PHE 0.015 0.001 PHE F 244 TYR 0.012 0.001 TYR A 332 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 190 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8564 (mtt) cc_final: 0.8197 (tmm) REVERT: A 359 GLU cc_start: 0.7221 (pm20) cc_final: 0.6889 (tm-30) REVERT: B 288 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8629 (t0) REVERT: B 325 TYR cc_start: 0.8722 (t80) cc_final: 0.8398 (t80) REVERT: C 48 THR cc_start: 0.8355 (m) cc_final: 0.8123 (p) REVERT: C 161 LEU cc_start: 0.8788 (mm) cc_final: 0.8492 (mm) REVERT: D 161 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7627 (pp) REVERT: E 162 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8769 (mmtm) REVERT: E 348 LEU cc_start: 0.8804 (tp) cc_final: 0.8548 (tp) REVERT: F 249 LYS cc_start: 0.9200 (tptt) cc_final: 0.8674 (pttt) REVERT: F 381 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7987 (mm-40) outliers start: 62 outliers final: 48 residues processed: 233 average time/residue: 0.2466 time to fit residues: 89.2212 Evaluate side-chains 233 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 183 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 381 GLN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16473 Z= 0.216 Angle : 0.534 8.955 22222 Z= 0.290 Chirality : 0.040 0.178 2408 Planarity : 0.004 0.025 2673 Dihedral : 6.739 61.394 2298 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.89 % Allowed : 17.35 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1842 helix: 0.90 (0.16), residues: 1218 sheet: 1.58 (0.49), residues: 96 loop : -1.51 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 143 HIS 0.010 0.001 HIS B 253 PHE 0.013 0.001 PHE C 144 TYR 0.014 0.001 TYR A 332 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 190 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 337 MET cc_start: 0.8552 (mtt) cc_final: 0.8190 (tmm) REVERT: A 359 GLU cc_start: 0.7201 (pm20) cc_final: 0.6786 (tm-30) REVERT: B 288 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8735 (t0) REVERT: B 325 TYR cc_start: 0.8761 (t80) cc_final: 0.8464 (t80) REVERT: C 50 ASP cc_start: 0.6033 (t0) cc_final: 0.5793 (t0) REVERT: C 161 LEU cc_start: 0.8877 (mm) cc_final: 0.8592 (mm) REVERT: C 330 ILE cc_start: 0.9577 (mm) cc_final: 0.9318 (tt) REVERT: D 161 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7692 (pp) REVERT: E 162 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8726 (mmtm) REVERT: E 288 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8789 (m-40) REVERT: F 249 LYS cc_start: 0.9199 (tptt) cc_final: 0.8629 (pttt) REVERT: F 328 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (tt) REVERT: F 381 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8058 (mm-40) outliers start: 68 outliers final: 50 residues processed: 237 average time/residue: 0.2577 time to fit residues: 93.7018 Evaluate side-chains 234 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16473 Z= 0.146 Angle : 0.513 9.918 22222 Z= 0.278 Chirality : 0.039 0.157 2408 Planarity : 0.004 0.031 2673 Dihedral : 6.378 60.880 2298 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.38 % Allowed : 18.44 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1842 helix: 0.94 (0.16), residues: 1218 sheet: 1.68 (0.50), residues: 96 loop : -1.43 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 143 HIS 0.016 0.001 HIS B 253 PHE 0.010 0.001 PHE C 136 TYR 0.012 0.001 TYR A 332 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 199 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8545 (mtt) cc_final: 0.8186 (tmm) REVERT: A 359 GLU cc_start: 0.7105 (pm20) cc_final: 0.6747 (tm-30) REVERT: B 288 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8677 (t0) REVERT: B 325 TYR cc_start: 0.8705 (t80) cc_final: 0.8411 (t80) REVERT: C 161 LEU cc_start: 0.8852 (mm) cc_final: 0.8565 (mm) REVERT: C 330 ILE cc_start: 0.9549 (mm) cc_final: 0.9313 (tt) REVERT: D 161 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7740 (pp) REVERT: E 288 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8810 (m-40) REVERT: F 249 LYS cc_start: 0.9180 (tptt) cc_final: 0.8718 (pptt) REVERT: F 328 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8121 (tt) REVERT: F 381 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8082 (mm-40) outliers start: 59 outliers final: 45 residues processed: 237 average time/residue: 0.2440 time to fit residues: 90.0940 Evaluate side-chains 238 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16473 Z= 0.189 Angle : 0.531 9.883 22222 Z= 0.286 Chirality : 0.040 0.244 2408 Planarity : 0.004 0.026 2673 Dihedral : 6.305 60.781 2298 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.61 % Allowed : 18.90 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1842 helix: 0.90 (0.16), residues: 1224 sheet: 1.76 (0.50), residues: 96 loop : -1.47 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 143 HIS 0.012 0.001 HIS B 253 PHE 0.011 0.001 PHE E 244 TYR 0.013 0.001 TYR A 332 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 185 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8558 (mtt) cc_final: 0.8188 (tmm) REVERT: A 359 GLU cc_start: 0.7116 (pm20) cc_final: 0.6724 (tm-30) REVERT: B 288 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8754 (t0) REVERT: B 325 TYR cc_start: 0.8710 (t80) cc_final: 0.8421 (t80) REVERT: C 161 LEU cc_start: 0.8862 (mm) cc_final: 0.8580 (mm) REVERT: C 330 ILE cc_start: 0.9554 (mm) cc_final: 0.9350 (tt) REVERT: D 161 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7790 (pp) REVERT: D 408 ASN cc_start: 0.6315 (m110) cc_final: 0.5903 (p0) REVERT: F 249 LYS cc_start: 0.9200 (tptt) cc_final: 0.8674 (pttt) REVERT: F 328 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8114 (tt) REVERT: F 381 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8121 (mm-40) outliers start: 63 outliers final: 55 residues processed: 228 average time/residue: 0.2588 time to fit residues: 91.2857 Evaluate side-chains 239 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.4980 chunk 171 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16473 Z= 0.155 Angle : 0.523 9.043 22222 Z= 0.281 Chirality : 0.039 0.181 2408 Planarity : 0.004 0.028 2673 Dihedral : 6.096 60.018 2298 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.38 % Allowed : 19.13 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1842 helix: 0.92 (0.16), residues: 1224 sheet: 1.83 (0.50), residues: 96 loop : -1.28 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 143 HIS 0.015 0.001 HIS B 253 PHE 0.010 0.001 PHE E 244 TYR 0.012 0.001 TYR A 332 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8555 (mtt) cc_final: 0.8180 (tmm) REVERT: A 359 GLU cc_start: 0.7134 (pm20) cc_final: 0.6752 (tm-30) REVERT: B 143 TRP cc_start: 0.8480 (t60) cc_final: 0.8058 (t60) REVERT: B 288 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8691 (t0) REVERT: B 325 TYR cc_start: 0.8664 (t80) cc_final: 0.8391 (t80) REVERT: C 161 LEU cc_start: 0.8855 (mm) cc_final: 0.8569 (mm) REVERT: D 399 GLU cc_start: 0.8544 (mp0) cc_final: 0.7764 (mp0) REVERT: D 408 ASN cc_start: 0.6329 (m110) cc_final: 0.5928 (p0) REVERT: E 18 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.7637 (ptp90) REVERT: F 249 LYS cc_start: 0.9206 (tptt) cc_final: 0.8731 (pptt) REVERT: F 328 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8107 (tt) outliers start: 59 outliers final: 53 residues processed: 236 average time/residue: 0.2519 time to fit residues: 91.7379 Evaluate side-chains 242 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 187 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16473 Z= 0.149 Angle : 0.526 8.894 22222 Z= 0.283 Chirality : 0.039 0.192 2408 Planarity : 0.004 0.027 2673 Dihedral : 5.938 59.150 2298 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.49 % Allowed : 18.96 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1842 helix: 0.95 (0.16), residues: 1224 sheet: 1.92 (0.50), residues: 96 loop : -1.26 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 342 HIS 0.013 0.001 HIS B 253 PHE 0.009 0.001 PHE C 291 TYR 0.012 0.001 TYR A 332 ARG 0.002 0.000 ARG C 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 ASN cc_start: 0.9226 (t0) cc_final: 0.8379 (t0) REVERT: A 359 GLU cc_start: 0.7220 (pm20) cc_final: 0.6846 (tm-30) REVERT: B 143 TRP cc_start: 0.8415 (t60) cc_final: 0.8093 (t60) REVERT: B 288 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8713 (t0) REVERT: C 161 LEU cc_start: 0.8816 (mm) cc_final: 0.8544 (mm) REVERT: D 238 GLU cc_start: 0.8525 (tp30) cc_final: 0.7590 (pp20) REVERT: D 399 GLU cc_start: 0.8495 (mp0) cc_final: 0.7740 (mp0) REVERT: D 408 ASN cc_start: 0.6293 (m110) cc_final: 0.5941 (p0) REVERT: E 18 ARG cc_start: 0.8143 (ptp-170) cc_final: 0.7621 (ptp90) REVERT: F 46 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8074 (tp40) REVERT: F 249 LYS cc_start: 0.9207 (tptt) cc_final: 0.8733 (pptt) REVERT: F 328 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8092 (tt) outliers start: 61 outliers final: 51 residues processed: 245 average time/residue: 0.2662 time to fit residues: 100.9823 Evaluate side-chains 250 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101714 restraints weight = 36430.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105004 restraints weight = 17391.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106542 restraints weight = 8973.722| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16473 Z= 0.166 Angle : 0.540 11.475 22222 Z= 0.289 Chirality : 0.039 0.182 2408 Planarity : 0.004 0.027 2673 Dihedral : 5.898 58.653 2298 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.26 % Allowed : 19.64 % 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: 0.56 (0.20), residues: 1842 helix: 0.95 (0.16), residues: 1224 sheet: 1.88 (0.50), residues: 96 loop : -1.24 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 342 HIS 0.010 0.001 HIS B 253 PHE 0.010 0.001 PHE C 136 TYR 0.035 0.001 TYR B 325 ARG 0.002 0.000 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2979.46 seconds wall clock time: 55 minutes 23.75 seconds (3323.75 seconds total)