Starting phenix.real_space_refine on Mon Apr 8 11:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/04_2024/6rb9_4789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/04_2024/6rb9_4789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/04_2024/6rb9_4789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/04_2024/6rb9_4789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/04_2024/6rb9_4789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/04_2024/6rb9_4789.pdb" } resolution = 3.2 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 8414 2.51 5 N 2212 2.21 5 O 2730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 250": "OD1" <-> "OD2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 250": "OD1" <-> "OD2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 250": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13391 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 7.03, per 1000 atoms: 0.52 Number of scatterers: 13391 At special positions: 0 Unit cell: (129.47, 129.47, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2730 8.00 N 2212 7.00 C 8414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.41 Conformation dependent library (CDL) restraints added in 2.4 seconds 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 22.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA A 48 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 50 " --> pdb=" O MET A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA B 48 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE B 50 " --> pdb=" O MET B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA C 48 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE C 50 " --> pdb=" O MET C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 50' Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 226 through 230 removed outlier: 5.471A pdb=" N LEU C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 removed outlier: 4.443A pdb=" N LEU D 23 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA D 48 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE D 50 " --> pdb=" O MET D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 50' Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU D 230 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 5.862A pdb=" N ALA E 48 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE E 50 " --> pdb=" O MET E 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 50' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 226 through 230 removed outlier: 5.471A pdb=" N LEU E 230 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET F 39 " --> pdb=" O TYR F 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 50 removed outlier: 5.862A pdb=" N ALA F 48 " --> pdb=" O ASN F 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE F 50 " --> pdb=" O MET F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 50' Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU F 230 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA G 48 " --> pdb=" O ASN G 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE G 50 " --> pdb=" O MET G 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 50' Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU G 230 " --> pdb=" O LYS G 227 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 588 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: 2.83 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4251 1.33 - 1.45: 1713 1.45 - 1.56: 7609 1.56 - 1.68: 0 1.68 - 1.80: 63 Bond restraints: 13636 Sorted by residual: bond pdb=" CB VAL F 192 " pdb=" CG1 VAL F 192 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL C 192 " pdb=" CG1 VAL C 192 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CB VAL E 192 " pdb=" CG1 VAL E 192 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL D 192 " pdb=" CG1 VAL D 192 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CB VAL B 192 " pdb=" CG1 VAL B 192 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 ... (remaining 13631 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.81: 341 106.81 - 113.60: 7697 113.60 - 120.39: 4742 120.39 - 127.18: 5711 127.18 - 133.97: 80 Bond angle restraints: 18571 Sorted by residual: angle pdb=" N LYS E 41 " pdb=" CA LYS E 41 " pdb=" C LYS E 41 " ideal model delta sigma weight residual 112.72 108.61 4.11 1.28e+00 6.10e-01 1.03e+01 angle pdb=" N LYS A 41 " pdb=" CA LYS A 41 " pdb=" C LYS A 41 " ideal model delta sigma weight residual 112.72 108.62 4.10 1.28e+00 6.10e-01 1.02e+01 angle pdb=" N LYS F 41 " pdb=" CA LYS F 41 " pdb=" C LYS F 41 " ideal model delta sigma weight residual 112.72 108.63 4.09 1.28e+00 6.10e-01 1.02e+01 angle pdb=" N LYS C 41 " pdb=" CA LYS C 41 " pdb=" C LYS C 41 " ideal model delta sigma weight residual 112.72 108.64 4.08 1.28e+00 6.10e-01 1.02e+01 angle pdb=" N LYS D 41 " pdb=" CA LYS D 41 " pdb=" C LYS D 41 " ideal model delta sigma weight residual 112.72 108.64 4.08 1.28e+00 6.10e-01 1.02e+01 ... (remaining 18566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.25: 6566 11.25 - 22.50: 1051 22.50 - 33.75: 419 33.75 - 44.99: 91 44.99 - 56.24: 42 Dihedral angle restraints: 8169 sinusoidal: 3073 harmonic: 5096 Sorted by residual: dihedral pdb=" CA ASN G 19 " pdb=" C ASN G 19 " pdb=" N VAL G 20 " pdb=" CA VAL G 20 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN C 19 " pdb=" C ASN C 19 " pdb=" N VAL C 20 " pdb=" CA VAL C 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN B 19 " pdb=" C ASN B 19 " pdb=" N VAL B 20 " pdb=" CA VAL B 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 927 0.029 - 0.058: 708 0.058 - 0.086: 285 0.086 - 0.115: 185 0.115 - 0.144: 51 Chirality restraints: 2156 Sorted by residual: chirality pdb=" CA VAL E 164 " pdb=" N VAL E 164 " pdb=" C VAL E 164 " pdb=" CB VAL E 164 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL F 164 " pdb=" N VAL F 164 " pdb=" C VAL F 164 " pdb=" CB VAL F 164 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2153 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 171 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 172 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 172 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 172 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 171 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 172 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 171 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO D 172 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " 0.025 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 196 2.62 - 3.19: 12496 3.19 - 3.76: 20246 3.76 - 4.33: 29230 4.33 - 4.90: 49372 Nonbonded interactions: 111540 Sorted by model distance: nonbonded pdb=" CE LYS F 130 " pdb=" OE1 GLU G 137 " model vdw 2.049 3.440 nonbonded pdb=" CE LYS D 130 " pdb=" OE1 GLU E 137 " model vdw 2.049 3.440 nonbonded pdb=" CE LYS B 130 " pdb=" OE1 GLU C 137 " model vdw 2.050 3.440 nonbonded pdb=" OE1 GLU A 137 " pdb=" CE LYS G 130 " model vdw 2.050 3.440 nonbonded pdb=" CE LYS C 130 " pdb=" OE1 GLU D 137 " model vdw 2.050 3.440 ... (remaining 111535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.210 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: 0.000 Extract box with map and model: 2.720 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.490 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.059 13636 Z= 0.651 Angle : 0.824 7.702 18571 Z= 0.463 Chirality : 0.051 0.144 2156 Planarity : 0.005 0.045 2415 Dihedral : 13.721 56.242 4907 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.85 % Favored : 84.15 % Rotamer: Outliers : 1.42 % Allowed : 12.46 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.15), residues: 1722 helix: -1.81 (0.32), residues: 140 sheet: -3.54 (0.18), residues: 595 loop : -4.22 (0.14), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP E 203 HIS 0.004 0.002 HIS G 162 PHE 0.028 0.003 PHE G 135 TYR 0.018 0.003 TYR G 84 ARG 0.003 0.001 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 276 time to evaluate : 1.583 Fit side-chains REVERT: A 68 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8309 (mttp) REVERT: A 205 GLU cc_start: 0.8130 (pp20) cc_final: 0.7344 (pt0) REVERT: B 68 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8344 (mttp) REVERT: B 77 MET cc_start: 0.8922 (mmt) cc_final: 0.8193 (mmt) REVERT: B 82 ASP cc_start: 0.8086 (m-30) cc_final: 0.7873 (m-30) REVERT: B 205 GLU cc_start: 0.8088 (pp20) cc_final: 0.7523 (pp20) REVERT: C 68 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8376 (mttp) REVERT: C 77 MET cc_start: 0.8948 (mmt) cc_final: 0.8382 (mmt) REVERT: C 81 GLU cc_start: 0.7578 (pm20) cc_final: 0.7227 (pm20) REVERT: C 205 GLU cc_start: 0.8196 (pp20) cc_final: 0.7911 (pp20) REVERT: D 21 ASP cc_start: 0.7753 (m-30) cc_final: 0.7470 (m-30) REVERT: D 68 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8483 (mttp) REVERT: D 205 GLU cc_start: 0.8197 (pp20) cc_final: 0.7516 (pt0) REVERT: E 68 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8327 (mttp) REVERT: E 81 GLU cc_start: 0.7707 (pm20) cc_final: 0.7469 (pm20) REVERT: E 205 GLU cc_start: 0.8090 (pp20) cc_final: 0.7495 (pt0) REVERT: F 25 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: F 68 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8278 (mttp) REVERT: F 205 GLU cc_start: 0.8085 (pp20) cc_final: 0.7742 (pp20) REVERT: G 39 MET cc_start: 0.4813 (mmm) cc_final: 0.4607 (mmp) REVERT: G 68 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8356 (mttp) REVERT: G 205 GLU cc_start: 0.8049 (pp20) cc_final: 0.7607 (pp20) outliers start: 21 outliers final: 13 residues processed: 297 average time/residue: 0.2101 time to fit residues: 97.1974 Evaluate side-chains 176 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13636 Z= 0.325 Angle : 0.624 6.381 18571 Z= 0.319 Chirality : 0.045 0.133 2156 Planarity : 0.005 0.041 2415 Dihedral : 5.918 65.234 1878 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 4.87 % Allowed : 19.09 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.17), residues: 1722 helix: 0.87 (0.43), residues: 140 sheet: -3.26 (0.16), residues: 805 loop : -3.87 (0.17), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 203 HIS 0.002 0.001 HIS A 162 PHE 0.019 0.002 PHE F 135 TYR 0.016 0.002 TYR F 244 ARG 0.001 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 172 time to evaluate : 2.023 Fit side-chains REVERT: A 64 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 68 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8250 (mttp) REVERT: A 205 GLU cc_start: 0.8142 (pp20) cc_final: 0.7878 (pp20) REVERT: C 64 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 68 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8309 (mttp) REVERT: C 81 GLU cc_start: 0.7397 (pm20) cc_final: 0.7062 (pm20) REVERT: C 130 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8097 (mtpp) REVERT: C 205 GLU cc_start: 0.8134 (pp20) cc_final: 0.7586 (pt0) REVERT: D 68 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8442 (mttp) REVERT: D 130 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8260 (mtmm) REVERT: D 205 GLU cc_start: 0.8223 (pp20) cc_final: 0.7560 (pp20) REVERT: E 68 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8336 (mttp) REVERT: E 81 GLU cc_start: 0.7593 (pm20) cc_final: 0.7378 (pm20) REVERT: E 130 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8123 (mttm) REVERT: E 205 GLU cc_start: 0.8177 (pp20) cc_final: 0.7514 (pt0) REVERT: F 68 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8248 (mttp) REVERT: F 205 GLU cc_start: 0.8145 (pp20) cc_final: 0.7320 (pp20) REVERT: G 39 MET cc_start: 0.4907 (mmm) cc_final: 0.4623 (mmp) REVERT: G 68 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8307 (mttp) REVERT: G 130 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8098 (mtpp) REVERT: G 205 GLU cc_start: 0.8100 (pp20) cc_final: 0.7606 (pp20) outliers start: 72 outliers final: 52 residues processed: 237 average time/residue: 0.2133 time to fit residues: 78.7269 Evaluate side-chains 216 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 162 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 233 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13636 Z= 0.303 Angle : 0.597 6.594 18571 Z= 0.306 Chirality : 0.045 0.136 2156 Planarity : 0.004 0.039 2415 Dihedral : 5.522 33.896 1875 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 7.72 % Allowed : 19.70 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.18), residues: 1722 helix: 1.72 (0.47), residues: 140 sheet: -2.96 (0.17), residues: 805 loop : -3.74 (0.17), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 203 HIS 0.002 0.001 HIS D 162 PHE 0.021 0.002 PHE B 62 TYR 0.016 0.002 TYR F 84 ARG 0.001 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 163 time to evaluate : 2.168 Fit side-chains REVERT: A 64 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8601 (mp) REVERT: A 68 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8329 (mttp) REVERT: A 205 GLU cc_start: 0.8188 (pp20) cc_final: 0.7892 (pp20) REVERT: A 230 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7662 (pp) REVERT: B 23 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7432 (mm) REVERT: B 64 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (mm) REVERT: B 230 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7900 (pp) REVERT: C 64 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 68 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8265 (mttp) REVERT: C 81 GLU cc_start: 0.7437 (pm20) cc_final: 0.7144 (pm20) REVERT: C 130 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8122 (mtpp) REVERT: C 205 GLU cc_start: 0.8110 (pp20) cc_final: 0.7793 (pp20) REVERT: C 230 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7754 (pp) REVERT: D 68 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8466 (mttp) REVERT: D 205 GLU cc_start: 0.8262 (pp20) cc_final: 0.7578 (pp20) REVERT: D 230 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7756 (pp) REVERT: E 68 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8336 (mttp) REVERT: E 81 GLU cc_start: 0.7598 (pm20) cc_final: 0.7391 (pm20) REVERT: E 130 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8179 (mttm) REVERT: E 205 GLU cc_start: 0.8212 (pp20) cc_final: 0.7442 (pt0) REVERT: F 68 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8231 (mttp) REVERT: F 205 GLU cc_start: 0.8146 (pp20) cc_final: 0.7291 (pp20) REVERT: G 68 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8302 (mttp) REVERT: G 130 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8084 (mttm) REVERT: G 205 GLU cc_start: 0.8098 (pp20) cc_final: 0.7473 (pp20) outliers start: 114 outliers final: 90 residues processed: 269 average time/residue: 0.2116 time to fit residues: 91.5535 Evaluate side-chains 245 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 147 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 233 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 187 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13636 Z= 0.197 Angle : 0.532 6.059 18571 Z= 0.273 Chirality : 0.043 0.132 2156 Planarity : 0.004 0.039 2415 Dihedral : 5.119 32.139 1875 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 6.43 % Allowed : 21.80 % Favored : 71.77 % 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: -4.02 (0.19), residues: 1722 helix: 2.40 (0.48), residues: 133 sheet: -2.65 (0.17), residues: 805 loop : -3.57 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 203 HIS 0.001 0.001 HIS A 119 PHE 0.016 0.002 PHE D 135 TYR 0.015 0.001 TYR F 244 ARG 0.001 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 167 time to evaluate : 1.715 Fit side-chains REVERT: A 64 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 68 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8257 (mttp) REVERT: A 154 ASN cc_start: 0.8361 (p0) cc_final: 0.8035 (p0) REVERT: A 205 GLU cc_start: 0.8096 (pp20) cc_final: 0.7393 (pp20) REVERT: A 230 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7599 (pp) REVERT: B 64 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8306 (mm) REVERT: B 230 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7864 (pp) REVERT: C 64 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8624 (mp) REVERT: C 68 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8180 (mttp) REVERT: C 81 GLU cc_start: 0.7243 (pm20) cc_final: 0.7012 (pm20) REVERT: C 130 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8136 (mtpp) REVERT: C 205 GLU cc_start: 0.8121 (pp20) cc_final: 0.7792 (pp20) REVERT: C 230 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7679 (pp) REVERT: D 68 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8426 (mttp) REVERT: D 187 ASN cc_start: 0.8221 (p0) cc_final: 0.7620 (p0) REVERT: D 205 GLU cc_start: 0.8216 (pp20) cc_final: 0.7432 (pp20) REVERT: D 230 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7769 (pp) REVERT: E 68 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8325 (mttp) REVERT: E 178 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7380 (tt0) REVERT: F 68 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8182 (mttp) REVERT: F 187 ASN cc_start: 0.8183 (p0) cc_final: 0.7687 (p0) REVERT: F 205 GLU cc_start: 0.8154 (pp20) cc_final: 0.7265 (pp20) REVERT: G 68 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8300 (mttp) REVERT: G 130 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8089 (mttm) outliers start: 95 outliers final: 74 residues processed: 254 average time/residue: 0.1960 time to fit residues: 79.3994 Evaluate side-chains 229 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 148 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13636 Z= 0.350 Angle : 0.588 6.701 18571 Z= 0.300 Chirality : 0.045 0.141 2156 Planarity : 0.004 0.037 2415 Dihedral : 5.286 35.761 1874 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 9.48 % Allowed : 19.77 % Favored : 70.75 % 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: -3.90 (0.19), residues: 1722 helix: 2.62 (0.47), residues: 133 sheet: -2.58 (0.18), residues: 805 loop : -3.51 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 203 HIS 0.002 0.001 HIS D 162 PHE 0.020 0.002 PHE B 135 TYR 0.016 0.002 TYR F 84 ARG 0.001 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 143 time to evaluate : 1.690 Fit side-chains REVERT: A 64 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 68 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8341 (mttp) REVERT: A 205 GLU cc_start: 0.8228 (pp20) cc_final: 0.7450 (pp20) REVERT: A 230 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7741 (pp) REVERT: B 23 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7505 (mm) REVERT: B 64 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8418 (mm) REVERT: B 230 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7922 (pp) REVERT: C 68 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8291 (mttp) REVERT: C 81 GLU cc_start: 0.7450 (pm20) cc_final: 0.7132 (pm20) REVERT: C 130 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8159 (mtpp) REVERT: C 230 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7660 (pp) REVERT: D 68 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8460 (mttp) REVERT: D 187 ASN cc_start: 0.8355 (p0) cc_final: 0.7814 (p0) REVERT: D 230 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7821 (pp) REVERT: E 68 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8348 (mttp) REVERT: E 236 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7892 (pt) REVERT: F 68 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8242 (mttp) REVERT: F 187 ASN cc_start: 0.8381 (p0) cc_final: 0.7879 (p0) REVERT: G 68 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8333 (mttp) REVERT: G 130 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8041 (mttm) outliers start: 140 outliers final: 120 residues processed: 274 average time/residue: 0.1811 time to fit residues: 80.6139 Evaluate side-chains 269 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 141 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 237 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13636 Z= 0.242 Angle : 0.547 6.062 18571 Z= 0.279 Chirality : 0.043 0.132 2156 Planarity : 0.004 0.038 2415 Dihedral : 5.126 35.626 1874 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 9.48 % Allowed : 20.38 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1722 helix: 2.69 (0.48), residues: 133 sheet: -2.41 (0.18), residues: 805 loop : -3.49 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 203 HIS 0.002 0.001 HIS D 162 PHE 0.017 0.002 PHE E 135 TYR 0.015 0.002 TYR F 244 ARG 0.001 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 159 time to evaluate : 1.643 Fit side-chains REVERT: A 64 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 68 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8297 (mttp) REVERT: A 205 GLU cc_start: 0.8201 (pp20) cc_final: 0.7405 (pp20) REVERT: A 230 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7701 (pp) REVERT: B 23 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7482 (mm) REVERT: B 64 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (mm) REVERT: B 77 MET cc_start: 0.8860 (mmt) cc_final: 0.8290 (mmt) REVERT: B 230 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7876 (pp) REVERT: C 68 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8213 (mttp) REVERT: C 81 GLU cc_start: 0.7276 (pm20) cc_final: 0.7039 (pm20) REVERT: C 130 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8377 (mtpp) REVERT: C 230 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7627 (pp) REVERT: D 64 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8523 (mm) REVERT: D 68 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8431 (mttp) REVERT: D 187 ASN cc_start: 0.8294 (p0) cc_final: 0.7708 (p0) REVERT: D 230 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7763 (pp) REVERT: E 68 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8343 (mttp) REVERT: E 236 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7905 (pt) REVERT: F 68 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8224 (mttp) REVERT: F 187 ASN cc_start: 0.8293 (p0) cc_final: 0.7783 (p0) REVERT: G 47 MET cc_start: 0.3081 (mmp) cc_final: 0.2754 (mmp) REVERT: G 68 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8351 (mttp) REVERT: G 130 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8040 (mttm) outliers start: 140 outliers final: 117 residues processed: 289 average time/residue: 0.1885 time to fit residues: 89.1232 Evaluate side-chains 274 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 148 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13636 Z= 0.206 Angle : 0.530 7.112 18571 Z= 0.270 Chirality : 0.043 0.129 2156 Planarity : 0.004 0.038 2415 Dihedral : 4.905 35.430 1874 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 9.68 % Allowed : 20.58 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.20), residues: 1722 helix: 2.53 (0.47), residues: 133 sheet: -2.25 (0.18), residues: 812 loop : -3.43 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 203 HIS 0.001 0.001 HIS D 162 PHE 0.016 0.002 PHE E 135 TYR 0.014 0.001 TYR F 244 ARG 0.001 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 166 time to evaluate : 1.455 Fit side-chains REVERT: A 64 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 68 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8242 (mttp) REVERT: A 154 ASN cc_start: 0.8299 (p0) cc_final: 0.7978 (p0) REVERT: A 205 GLU cc_start: 0.8169 (pp20) cc_final: 0.7405 (pp20) REVERT: A 230 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7682 (pp) REVERT: B 23 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7462 (mm) REVERT: B 64 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 230 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7876 (pp) REVERT: C 47 MET cc_start: 0.3863 (mmp) cc_final: 0.3654 (mmm) REVERT: C 68 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8174 (mttp) REVERT: C 81 GLU cc_start: 0.7238 (pm20) cc_final: 0.7005 (pm20) REVERT: C 130 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8368 (mtpp) REVERT: C 154 ASN cc_start: 0.8311 (p0) cc_final: 0.8098 (p0) REVERT: C 230 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7597 (pp) REVERT: D 64 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8505 (mm) REVERT: D 68 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8430 (mttp) REVERT: D 154 ASN cc_start: 0.8139 (p0) cc_final: 0.7872 (p0) REVERT: D 187 ASN cc_start: 0.8184 (p0) cc_final: 0.7569 (p0) REVERT: D 230 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7766 (pp) REVERT: E 68 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8324 (mttp) REVERT: E 236 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7897 (pt) REVERT: F 68 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8203 (mttp) REVERT: F 187 ASN cc_start: 0.8220 (p0) cc_final: 0.7753 (p0) REVERT: G 68 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8300 (mttp) REVERT: G 130 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8066 (mttm) outliers start: 143 outliers final: 126 residues processed: 298 average time/residue: 0.1940 time to fit residues: 91.8546 Evaluate side-chains 299 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 164 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13636 Z= 0.183 Angle : 0.521 7.878 18571 Z= 0.266 Chirality : 0.043 0.141 2156 Planarity : 0.004 0.038 2415 Dihedral : 4.752 34.444 1874 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 9.61 % Allowed : 20.65 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.20), residues: 1722 helix: 2.42 (0.47), residues: 133 sheet: -2.10 (0.18), residues: 812 loop : -3.42 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 203 HIS 0.001 0.001 HIS D 162 PHE 0.016 0.001 PHE F 212 TYR 0.014 0.001 TYR F 244 ARG 0.003 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 171 time to evaluate : 1.583 Fit side-chains REVERT: A 64 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 68 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8253 (mttp) REVERT: A 154 ASN cc_start: 0.8274 (p0) cc_final: 0.7954 (p0) REVERT: A 205 GLU cc_start: 0.8160 (pp20) cc_final: 0.7473 (pt0) REVERT: A 230 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7683 (pp) REVERT: B 64 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 77 MET cc_start: 0.8851 (mmt) cc_final: 0.8282 (mmt) REVERT: B 230 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7780 (pp) REVERT: B 236 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7693 (pt) REVERT: C 68 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8152 (mttp) REVERT: C 81 GLU cc_start: 0.7213 (pm20) cc_final: 0.6995 (pm20) REVERT: C 130 LYS cc_start: 0.8716 (mtmm) cc_final: 0.7969 (mtpp) REVERT: C 154 ASN cc_start: 0.8260 (p0) cc_final: 0.8053 (p0) REVERT: C 230 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7578 (pp) REVERT: D 64 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8509 (mm) REVERT: D 68 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8412 (mttp) REVERT: D 154 ASN cc_start: 0.8102 (p0) cc_final: 0.7835 (p0) REVERT: D 187 ASN cc_start: 0.8132 (p0) cc_final: 0.7497 (p0) REVERT: D 230 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7756 (pp) REVERT: E 68 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8307 (mttp) REVERT: E 236 ILE cc_start: 0.8195 (pt) cc_final: 0.7903 (pt) REVERT: F 68 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8237 (mttp) REVERT: F 187 ASN cc_start: 0.8181 (p0) cc_final: 0.7706 (p0) REVERT: F 205 GLU cc_start: 0.8294 (pp20) cc_final: 0.7760 (pp20) REVERT: G 39 MET cc_start: 0.3956 (mmm) cc_final: 0.3740 (mmm) REVERT: G 68 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8299 (mttp) REVERT: G 130 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8049 (mttm) outliers start: 142 outliers final: 123 residues processed: 304 average time/residue: 0.1904 time to fit residues: 92.6428 Evaluate side-chains 302 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 171 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 237 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 0.0000 chunk 159 optimal weight: 0.1980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 243 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN G 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13636 Z= 0.154 Angle : 0.507 8.826 18571 Z= 0.261 Chirality : 0.042 0.138 2156 Planarity : 0.004 0.048 2415 Dihedral : 4.387 30.285 1872 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 7.58 % Allowed : 22.48 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.20), residues: 1722 helix: 2.32 (0.48), residues: 133 sheet: -1.87 (0.19), residues: 812 loop : -3.36 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 203 HIS 0.001 0.000 HIS B 162 PHE 0.014 0.001 PHE E 135 TYR 0.014 0.001 TYR F 244 ARG 0.001 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 189 time to evaluate : 1.458 Fit side-chains REVERT: A 64 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8558 (mp) REVERT: A 68 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8274 (mttp) REVERT: A 154 ASN cc_start: 0.8231 (p0) cc_final: 0.7925 (p0) REVERT: A 205 GLU cc_start: 0.8153 (pp20) cc_final: 0.7513 (pt0) REVERT: A 230 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7698 (pp) REVERT: B 77 MET cc_start: 0.8832 (mmt) cc_final: 0.8275 (mmt) REVERT: B 230 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8033 (pp) REVERT: C 68 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8151 (mttp) REVERT: C 77 MET cc_start: 0.8624 (mmt) cc_final: 0.8004 (mmt) REVERT: C 130 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8203 (mtpp) REVERT: C 178 GLU cc_start: 0.7578 (tt0) cc_final: 0.7315 (tt0) REVERT: C 230 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7468 (pp) REVERT: D 64 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8357 (mm) REVERT: D 68 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8359 (mttp) REVERT: D 77 MET cc_start: 0.8652 (mmt) cc_final: 0.8145 (mmt) REVERT: D 154 ASN cc_start: 0.8020 (p0) cc_final: 0.7779 (p0) REVERT: D 187 ASN cc_start: 0.8026 (p0) cc_final: 0.7678 (p0) REVERT: D 230 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7762 (pp) REVERT: E 68 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8277 (mttp) REVERT: E 154 ASN cc_start: 0.8113 (p0) cc_final: 0.7912 (p0) REVERT: E 236 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7832 (pt) REVERT: F 68 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8074 (mttp) REVERT: G 68 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8359 (mttp) REVERT: G 130 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8017 (mttm) REVERT: G 154 ASN cc_start: 0.8119 (p0) cc_final: 0.7702 (p0) outliers start: 112 outliers final: 100 residues processed: 292 average time/residue: 0.1981 time to fit residues: 91.8002 Evaluate side-chains 288 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 181 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 237 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 0.0170 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13636 Z= 0.207 Angle : 0.541 9.608 18571 Z= 0.279 Chirality : 0.043 0.151 2156 Planarity : 0.004 0.046 2415 Dihedral : 4.345 32.295 1865 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 8.06 % Allowed : 22.21 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1722 helix: 2.42 (0.48), residues: 133 sheet: -1.72 (0.19), residues: 812 loop : -3.34 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 203 HIS 0.001 0.001 HIS D 162 PHE 0.016 0.002 PHE D 135 TYR 0.013 0.001 TYR F 244 ARG 0.001 0.000 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 183 time to evaluate : 1.590 Fit side-chains REVERT: A 64 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 68 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8288 (mttp) REVERT: A 154 ASN cc_start: 0.8255 (p0) cc_final: 0.7953 (p0) REVERT: A 203 TRP cc_start: 0.8029 (p90) cc_final: 0.7664 (p90) REVERT: A 205 GLU cc_start: 0.8176 (pp20) cc_final: 0.7518 (pt0) REVERT: A 230 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7695 (pp) REVERT: B 77 MET cc_start: 0.8833 (mmt) cc_final: 0.8279 (mmt) REVERT: B 230 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8072 (pp) REVERT: C 68 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8126 (mttp) REVERT: C 77 MET cc_start: 0.8659 (mmt) cc_final: 0.8013 (mmt) REVERT: C 81 GLU cc_start: 0.7470 (pm20) cc_final: 0.7024 (pm20) REVERT: C 130 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8156 (mtpp) REVERT: C 178 GLU cc_start: 0.7632 (tt0) cc_final: 0.7355 (tt0) REVERT: C 230 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7607 (pp) REVERT: D 64 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8504 (mm) REVERT: D 68 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8357 (mttp) REVERT: D 154 ASN cc_start: 0.8059 (p0) cc_final: 0.7821 (p0) REVERT: D 187 ASN cc_start: 0.8107 (p0) cc_final: 0.7474 (p0) REVERT: D 230 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7778 (pp) REVERT: E 68 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8294 (mttp) REVERT: E 154 ASN cc_start: 0.8136 (p0) cc_final: 0.7910 (p0) REVERT: E 236 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7917 (pt) REVERT: F 68 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8025 (mttp) REVERT: F 187 ASN cc_start: 0.8149 (p0) cc_final: 0.7645 (p0) REVERT: G 68 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8363 (mttp) REVERT: G 154 ASN cc_start: 0.8150 (p0) cc_final: 0.7744 (p0) REVERT: G 203 TRP cc_start: 0.7961 (p90) cc_final: 0.7568 (p90) outliers start: 119 outliers final: 111 residues processed: 294 average time/residue: 0.1863 time to fit residues: 87.5334 Evaluate side-chains 299 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 181 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 237 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112290 restraints weight = 16453.277| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.81 r_work: 0.3246 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 13636 Z= 0.270 Angle : 0.776 59.200 18571 Z= 0.449 Chirality : 0.048 0.930 2156 Planarity : 0.004 0.046 2415 Dihedral : 4.388 32.317 1865 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 8.60 % Allowed : 21.67 % Favored : 69.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1722 helix: 2.42 (0.48), residues: 133 sheet: -1.69 (0.19), residues: 812 loop : -3.34 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 203 HIS 0.001 0.001 HIS D 162 PHE 0.021 0.002 PHE D 212 TYR 0.013 0.001 TYR F 244 ARG 0.001 0.000 ARG B 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2936.09 seconds wall clock time: 54 minutes 57.74 seconds (3297.74 seconds total)