Starting phenix.real_space_refine on Thu Feb 15 07:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmw_0922/02_2024/6lmw_0922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmw_0922/02_2024/6lmw_0922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmw_0922/02_2024/6lmw_0922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmw_0922/02_2024/6lmw_0922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmw_0922/02_2024/6lmw_0922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmw_0922/02_2024/6lmw_0922.pdb" } resolution = 3.4 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 136 5.16 5 C 7608 2.51 5 N 1888 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 133": "OD1" <-> "OD2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 133": "OD1" <-> "OD2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 133": "OD1" <-> "OD2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11624 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.21, per 1000 atoms: 0.53 Number of scatterers: 11624 At special positions: 0 Unit cell: (125.823, 125.823, 87.6519, 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 136 16.00 O 1992 8.00 N 1888 7.00 C 7608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 160 " distance=2.02 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: 4.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 166 through 203 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.808A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.671A pdb=" N PHE B 137 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 166 through 203 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 166 through 203 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE D 137 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 166 through 203 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 47 through 70 removed outlier: 3.628A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.810A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE E 137 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 166 through 203 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE F 137 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 166 through 203 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.810A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 121 Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE G 137 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 166 through 203 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.808A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 121 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE H 137 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 166 through 203 793 hydrogen bonds defined for protein. 2355 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: 2.86 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3484 1.34 - 1.46: 2594 1.46 - 1.58: 5618 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 11904 Sorted by residual: bond pdb=" CB THR B 117 " pdb=" CG2 THR B 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR H 117 " pdb=" CG2 THR H 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR D 117 " pdb=" CG2 THR D 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR F 117 " pdb=" CG2 THR F 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR A 117 " pdb=" CG2 THR A 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 ... (remaining 11899 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.24: 398 106.24 - 113.59: 6392 113.59 - 120.95: 6529 120.95 - 128.30: 2681 128.30 - 135.66: 120 Bond angle restraints: 16120 Sorted by residual: angle pdb=" CA PRO E 59 " pdb=" C PRO E 59 " pdb=" N PRO E 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO C 59 " pdb=" C PRO C 59 " pdb=" N PRO C 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO A 59 " pdb=" C PRO A 59 " pdb=" N PRO A 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO G 59 " pdb=" C PRO G 59 " pdb=" N PRO G 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO B 59 " pdb=" C PRO B 59 " pdb=" N PRO B 60 " ideal model delta sigma weight residual 117.93 121.92 -3.99 1.20e+00 6.94e-01 1.11e+01 ... (remaining 16115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6287 17.18 - 34.37: 729 34.37 - 51.55: 112 51.55 - 68.73: 16 68.73 - 85.91: 24 Dihedral angle restraints: 7168 sinusoidal: 2872 harmonic: 4296 Sorted by residual: dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 160 " pdb=" CB CYS F 160 " ideal model delta sinusoidal sigma weight residual 93.00 120.01 -27.01 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CB CYS H 43 " pdb=" SG CYS H 43 " pdb=" SG CYS H 160 " pdb=" CB CYS H 160 " ideal model delta sinusoidal sigma weight residual 93.00 120.01 -27.01 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CB CYS A 43 " pdb=" SG CYS A 43 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 120.00 -27.00 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 7165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 861 0.030 - 0.060: 674 0.060 - 0.090: 201 0.090 - 0.120: 60 0.120 - 0.150: 44 Chirality restraints: 1840 Sorted by residual: chirality pdb=" CB VAL G 74 " pdb=" CA VAL G 74 " pdb=" CG1 VAL G 74 " pdb=" CG2 VAL G 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CB VAL D 74 " pdb=" CA VAL D 74 " pdb=" CG1 VAL D 74 " pdb=" CG2 VAL D 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1837 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO D 60 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 59 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO F 60 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.052 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO B 60 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.044 5.00e-02 4.00e+02 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3467 2.81 - 3.33: 10472 3.33 - 3.86: 18446 3.86 - 4.38: 21314 4.38 - 4.90: 37158 Nonbonded interactions: 90857 Sorted by model distance: nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 181 " model vdw 2.292 2.440 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 181 " model vdw 2.292 2.440 nonbonded pdb=" O LEU A 118 " pdb=" OG SER A 181 " model vdw 2.292 2.440 nonbonded pdb=" O LEU C 118 " pdb=" OG SER C 181 " model vdw 2.292 2.440 nonbonded pdb=" O LEU H 118 " pdb=" OG SER H 181 " model vdw 2.292 2.440 ... (remaining 90852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.940 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.530 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.007 0.081 11904 Z= 0.431 Angle : 0.912 10.656 16120 Z= 0.479 Chirality : 0.047 0.150 1840 Planarity : 0.008 0.077 1984 Dihedral : 15.334 85.915 4336 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.63 % Allowed : 6.92 % Favored : 92.45 % 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: -5.34 (0.13), residues: 1456 helix: -3.84 (0.07), residues: 992 sheet: None (None), residues: 0 loop : -2.24 (0.22), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 62 PHE 0.009 0.002 PHE A 68 TYR 0.008 0.002 TYR D 34 ARG 0.008 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7967 (ttt) cc_final: 0.7719 (ttt) REVERT: A 192 MET cc_start: 0.6773 (ttp) cc_final: 0.6414 (ttt) REVERT: B 49 TYR cc_start: 0.8213 (t80) cc_final: 0.7986 (t80) REVERT: B 153 LYS cc_start: 0.8610 (mttt) cc_final: 0.7897 (mtpp) REVERT: B 176 TYR cc_start: 0.8062 (t80) cc_final: 0.7750 (t80) REVERT: B 192 MET cc_start: 0.6397 (ttp) cc_final: 0.6118 (ttt) REVERT: C 33 MET cc_start: 0.7967 (ttt) cc_final: 0.7694 (ttt) REVERT: C 192 MET cc_start: 0.6779 (ttp) cc_final: 0.6420 (ttt) REVERT: D 49 TYR cc_start: 0.8212 (t80) cc_final: 0.7988 (t80) REVERT: D 153 LYS cc_start: 0.8608 (mttt) cc_final: 0.7897 (mtpp) REVERT: D 176 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80) REVERT: D 192 MET cc_start: 0.6397 (ttp) cc_final: 0.6119 (ttt) REVERT: E 33 MET cc_start: 0.7968 (ttt) cc_final: 0.7693 (ttt) REVERT: E 192 MET cc_start: 0.6777 (ttp) cc_final: 0.6416 (ttt) REVERT: F 49 TYR cc_start: 0.8209 (t80) cc_final: 0.7986 (t80) REVERT: F 153 LYS cc_start: 0.8610 (mttt) cc_final: 0.7897 (mtpp) REVERT: F 176 TYR cc_start: 0.8073 (t80) cc_final: 0.7760 (t80) REVERT: F 192 MET cc_start: 0.6403 (ttp) cc_final: 0.6112 (ttt) REVERT: G 33 MET cc_start: 0.7968 (ttt) cc_final: 0.7720 (ttt) REVERT: G 192 MET cc_start: 0.6770 (ttp) cc_final: 0.6411 (ttt) REVERT: H 49 TYR cc_start: 0.8207 (t80) cc_final: 0.7985 (t80) REVERT: H 153 LYS cc_start: 0.8608 (mttt) cc_final: 0.7897 (mtpp) REVERT: H 176 TYR cc_start: 0.8064 (t80) cc_final: 0.7751 (t80) REVERT: H 192 MET cc_start: 0.6403 (ttp) cc_final: 0.6109 (ttt) outliers start: 8 outliers final: 8 residues processed: 244 average time/residue: 0.1993 time to fit residues: 72.1750 Evaluate side-chains 216 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN B 131 ASN C 71 ASN D 71 ASN D 131 ASN E 71 ASN F 71 ASN F 131 ASN G 71 ASN H 71 ASN H 131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11904 Z= 0.179 Angle : 0.600 7.786 16120 Z= 0.290 Chirality : 0.036 0.109 1840 Planarity : 0.006 0.057 1984 Dihedral : 4.313 16.135 1600 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.81 % Allowed : 13.99 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1456 helix: -0.38 (0.14), residues: 1048 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 62 PHE 0.010 0.001 PHE B 68 TYR 0.014 0.001 TYR D 34 ARG 0.002 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 224 time to evaluate : 1.271 Fit side-chains REVERT: A 33 MET cc_start: 0.7914 (ttt) cc_final: 0.7700 (ttm) REVERT: A 46 GLU cc_start: 0.7846 (mp0) cc_final: 0.7167 (mp0) REVERT: A 48 ASN cc_start: 0.7600 (m-40) cc_final: 0.7393 (m110) REVERT: A 157 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6621 (mtp85) REVERT: A 192 MET cc_start: 0.6658 (ttp) cc_final: 0.6445 (ttt) REVERT: B 153 LYS cc_start: 0.8198 (mttt) cc_final: 0.7509 (mtpp) REVERT: B 176 TYR cc_start: 0.7613 (t80) cc_final: 0.7353 (t80) REVERT: B 192 MET cc_start: 0.6179 (ttp) cc_final: 0.5892 (ttt) REVERT: C 33 MET cc_start: 0.7918 (ttt) cc_final: 0.7708 (ttm) REVERT: C 46 GLU cc_start: 0.7839 (mp0) cc_final: 0.7159 (mp0) REVERT: C 48 ASN cc_start: 0.7595 (m-40) cc_final: 0.7388 (m110) REVERT: C 157 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6621 (mtp85) REVERT: C 192 MET cc_start: 0.6658 (ttp) cc_final: 0.6447 (ttt) REVERT: D 153 LYS cc_start: 0.8199 (mttt) cc_final: 0.7511 (mtpp) REVERT: D 176 TYR cc_start: 0.7625 (t80) cc_final: 0.7364 (t80) REVERT: D 192 MET cc_start: 0.6178 (ttp) cc_final: 0.5896 (ttt) REVERT: E 33 MET cc_start: 0.7914 (ttt) cc_final: 0.7703 (ttm) REVERT: E 46 GLU cc_start: 0.7842 (mp0) cc_final: 0.7162 (mp0) REVERT: E 48 ASN cc_start: 0.7604 (m-40) cc_final: 0.7396 (m110) REVERT: E 157 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6620 (mtp85) REVERT: E 192 MET cc_start: 0.6656 (ttp) cc_final: 0.6445 (ttt) REVERT: F 153 LYS cc_start: 0.8202 (mttt) cc_final: 0.7512 (mtpp) REVERT: F 176 TYR cc_start: 0.7629 (t80) cc_final: 0.7368 (t80) REVERT: F 192 MET cc_start: 0.6184 (ttp) cc_final: 0.5902 (ttt) REVERT: G 33 MET cc_start: 0.7917 (ttt) cc_final: 0.7708 (ttm) REVERT: G 46 GLU cc_start: 0.7843 (mp0) cc_final: 0.7161 (mp0) REVERT: G 48 ASN cc_start: 0.7603 (m-40) cc_final: 0.7395 (m110) REVERT: G 157 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6620 (mtp85) REVERT: G 192 MET cc_start: 0.6653 (ttp) cc_final: 0.6443 (ttt) REVERT: H 153 LYS cc_start: 0.8201 (mttt) cc_final: 0.7512 (mtpp) REVERT: H 176 TYR cc_start: 0.7619 (t80) cc_final: 0.7359 (t80) REVERT: H 192 MET cc_start: 0.6183 (ttp) cc_final: 0.5898 (ttt) outliers start: 23 outliers final: 12 residues processed: 228 average time/residue: 0.2399 time to fit residues: 76.5465 Evaluate side-chains 212 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11904 Z= 0.343 Angle : 0.671 7.749 16120 Z= 0.324 Chirality : 0.039 0.126 1840 Planarity : 0.006 0.058 1984 Dihedral : 4.276 14.033 1592 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.09 % Allowed : 15.25 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1456 helix: 0.70 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -1.47 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 186 PHE 0.010 0.002 PHE A 68 TYR 0.017 0.002 TYR B 34 ARG 0.002 0.000 ARG H 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 1.182 Fit side-chains REVERT: A 46 GLU cc_start: 0.7884 (mp0) cc_final: 0.7134 (mp0) REVERT: A 150 GLU cc_start: 0.8805 (mp0) cc_final: 0.7995 (mp0) REVERT: A 157 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.6670 (mtp85) REVERT: A 192 MET cc_start: 0.6643 (ttp) cc_final: 0.6412 (ttt) REVERT: B 153 LYS cc_start: 0.8204 (mttt) cc_final: 0.7549 (mtpp) REVERT: C 46 GLU cc_start: 0.7883 (mp0) cc_final: 0.7131 (mp0) REVERT: C 150 GLU cc_start: 0.8806 (mp0) cc_final: 0.7993 (mp0) REVERT: C 157 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6663 (mtp85) REVERT: C 192 MET cc_start: 0.6646 (ttp) cc_final: 0.6417 (ttt) REVERT: D 153 LYS cc_start: 0.8205 (mttt) cc_final: 0.7553 (mtpp) REVERT: E 46 GLU cc_start: 0.7881 (mp0) cc_final: 0.7107 (mp0) REVERT: E 150 GLU cc_start: 0.8806 (mp0) cc_final: 0.7992 (mp0) REVERT: E 157 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6665 (mtp85) REVERT: E 192 MET cc_start: 0.6644 (ttp) cc_final: 0.6414 (ttt) REVERT: F 153 LYS cc_start: 0.8209 (mttt) cc_final: 0.7554 (mtpp) REVERT: G 46 GLU cc_start: 0.7880 (mp0) cc_final: 0.7105 (mp0) REVERT: G 150 GLU cc_start: 0.8805 (mp0) cc_final: 0.7992 (mp0) REVERT: G 157 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6668 (mtp85) REVERT: G 192 MET cc_start: 0.6641 (ttp) cc_final: 0.6410 (ttt) REVERT: H 153 LYS cc_start: 0.8203 (mttt) cc_final: 0.7551 (mtpp) outliers start: 52 outliers final: 28 residues processed: 234 average time/residue: 0.2546 time to fit residues: 82.2384 Evaluate side-chains 230 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 0.0370 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11904 Z= 0.145 Angle : 0.559 7.608 16120 Z= 0.261 Chirality : 0.035 0.107 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.822 12.206 1592 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.07 % Allowed : 17.30 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1456 helix: 1.56 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.93 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 62 PHE 0.005 0.001 PHE E 39 TYR 0.010 0.001 TYR A 34 ARG 0.001 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 1.296 Fit side-chains REVERT: A 46 GLU cc_start: 0.8019 (mp0) cc_final: 0.7314 (mp0) REVERT: A 150 GLU cc_start: 0.8758 (mp0) cc_final: 0.8229 (mp0) REVERT: A 157 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6627 (mtp85) REVERT: B 119 MET cc_start: 0.7953 (mmp) cc_final: 0.7457 (mmp) REVERT: B 153 LYS cc_start: 0.8143 (mttt) cc_final: 0.7503 (mtpp) REVERT: B 176 TYR cc_start: 0.7692 (t80) cc_final: 0.7462 (t80) REVERT: C 46 GLU cc_start: 0.8012 (mp0) cc_final: 0.7306 (mp0) REVERT: C 150 GLU cc_start: 0.8755 (mp0) cc_final: 0.8229 (mp0) REVERT: C 157 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.6620 (mtp85) REVERT: D 119 MET cc_start: 0.7944 (mmp) cc_final: 0.7449 (mmp) REVERT: D 153 LYS cc_start: 0.8144 (mttt) cc_final: 0.7507 (mtpp) REVERT: E 46 GLU cc_start: 0.8019 (mp0) cc_final: 0.7279 (mp0) REVERT: E 150 GLU cc_start: 0.8755 (mp0) cc_final: 0.8228 (mp0) REVERT: E 157 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6627 (mtp85) REVERT: F 119 MET cc_start: 0.7952 (mmp) cc_final: 0.7454 (mmp) REVERT: F 153 LYS cc_start: 0.8148 (mttt) cc_final: 0.7507 (mtpp) REVERT: G 46 GLU cc_start: 0.8018 (mp0) cc_final: 0.7277 (mp0) REVERT: G 150 GLU cc_start: 0.8757 (mp0) cc_final: 0.8228 (mp0) REVERT: G 157 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6627 (mtp85) REVERT: H 119 MET cc_start: 0.7951 (mmp) cc_final: 0.7454 (mmp) REVERT: H 153 LYS cc_start: 0.8144 (mttt) cc_final: 0.7506 (mtpp) outliers start: 39 outliers final: 24 residues processed: 229 average time/residue: 0.2574 time to fit residues: 81.6415 Evaluate side-chains 236 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 0.0010 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11904 Z= 0.164 Angle : 0.568 7.634 16120 Z= 0.262 Chirality : 0.036 0.110 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.652 11.411 1592 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.17 % Allowed : 17.45 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1456 helix: 1.94 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.11 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 62 PHE 0.004 0.001 PHE H 154 TYR 0.010 0.001 TYR A 34 ARG 0.001 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 208 time to evaluate : 1.521 Fit side-chains REVERT: A 46 GLU cc_start: 0.8008 (mp0) cc_final: 0.7340 (mp0) REVERT: A 107 LEU cc_start: 0.7687 (mt) cc_final: 0.7451 (mp) REVERT: A 150 GLU cc_start: 0.8767 (mp0) cc_final: 0.8137 (mp0) REVERT: A 157 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6634 (mtp85) REVERT: B 119 MET cc_start: 0.7816 (mmp) cc_final: 0.7584 (mmt) REVERT: B 153 LYS cc_start: 0.8138 (mttt) cc_final: 0.7933 (ttmm) REVERT: C 46 GLU cc_start: 0.8001 (mp0) cc_final: 0.7331 (mp0) REVERT: C 150 GLU cc_start: 0.8766 (mp0) cc_final: 0.8135 (mp0) REVERT: C 157 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6628 (mtp85) REVERT: D 119 MET cc_start: 0.7814 (mmp) cc_final: 0.7585 (mmt) REVERT: D 153 LYS cc_start: 0.8142 (mttt) cc_final: 0.7935 (ttmm) REVERT: E 46 GLU cc_start: 0.8001 (mp0) cc_final: 0.7329 (mp0) REVERT: E 150 GLU cc_start: 0.8767 (mp0) cc_final: 0.8134 (mp0) REVERT: E 157 ARG cc_start: 0.7244 (mtm-85) cc_final: 0.6634 (mtp85) REVERT: F 119 MET cc_start: 0.7821 (mmp) cc_final: 0.7594 (mmt) REVERT: F 153 LYS cc_start: 0.8147 (mttt) cc_final: 0.7941 (ttmm) REVERT: G 46 GLU cc_start: 0.8002 (mp0) cc_final: 0.7330 (mp0) REVERT: G 150 GLU cc_start: 0.8768 (mp0) cc_final: 0.8133 (mp0) REVERT: G 157 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6633 (mtp85) REVERT: H 119 MET cc_start: 0.7820 (mmp) cc_final: 0.7593 (mmt) REVERT: H 153 LYS cc_start: 0.8140 (mttt) cc_final: 0.7935 (ttmm) outliers start: 53 outliers final: 42 residues processed: 236 average time/residue: 0.2601 time to fit residues: 84.5218 Evaluate side-chains 246 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11904 Z= 0.174 Angle : 0.565 7.564 16120 Z= 0.262 Chirality : 0.036 0.112 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.574 11.311 1592 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.35 % Allowed : 16.35 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1456 helix: 2.07 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.01 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 62 PHE 0.005 0.001 PHE D 197 TYR 0.013 0.001 TYR D 49 ARG 0.001 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 1.224 Fit side-chains REVERT: A 46 GLU cc_start: 0.7942 (mp0) cc_final: 0.7238 (mp0) REVERT: A 150 GLU cc_start: 0.8790 (mp0) cc_final: 0.7993 (mp0) REVERT: A 157 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.6717 (mtp85) REVERT: B 38 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: C 46 GLU cc_start: 0.7940 (mp0) cc_final: 0.7235 (mp0) REVERT: C 150 GLU cc_start: 0.8788 (mp0) cc_final: 0.7991 (mp0) REVERT: C 157 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6711 (mtp85) REVERT: D 38 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: E 46 GLU cc_start: 0.7944 (mp0) cc_final: 0.7238 (mp0) REVERT: E 150 GLU cc_start: 0.8789 (mp0) cc_final: 0.7991 (mp0) REVERT: E 157 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.6715 (mtp85) REVERT: F 38 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: G 46 GLU cc_start: 0.7937 (mp0) cc_final: 0.7231 (mp0) REVERT: G 150 GLU cc_start: 0.8788 (mp0) cc_final: 0.7991 (mp0) REVERT: G 157 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.6715 (mtp85) REVERT: H 38 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6714 (pm20) outliers start: 68 outliers final: 52 residues processed: 248 average time/residue: 0.2403 time to fit residues: 83.9982 Evaluate side-chains 252 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 196 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.0050 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11904 Z= 0.161 Angle : 0.559 7.552 16120 Z= 0.258 Chirality : 0.036 0.110 1840 Planarity : 0.005 0.050 1984 Dihedral : 3.514 10.959 1592 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.19 % Allowed : 16.59 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1456 helix: 2.22 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 62 PHE 0.004 0.001 PHE F 154 TYR 0.012 0.001 TYR F 49 ARG 0.001 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 200 time to evaluate : 1.264 Fit side-chains REVERT: A 46 GLU cc_start: 0.7952 (mp0) cc_final: 0.7249 (mp0) REVERT: A 150 GLU cc_start: 0.8768 (mp0) cc_final: 0.8040 (mp0) REVERT: A 157 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.6582 (mtp85) REVERT: B 38 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: B 119 MET cc_start: 0.7818 (mmp) cc_final: 0.7440 (mmp) REVERT: C 46 GLU cc_start: 0.7950 (mp0) cc_final: 0.7244 (mp0) REVERT: C 150 GLU cc_start: 0.8766 (mp0) cc_final: 0.8037 (mp0) REVERT: C 157 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.6574 (mtp85) REVERT: D 38 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: D 119 MET cc_start: 0.7814 (mmp) cc_final: 0.7439 (mmp) REVERT: E 46 GLU cc_start: 0.7950 (mp0) cc_final: 0.7241 (mp0) REVERT: E 150 GLU cc_start: 0.8767 (mp0) cc_final: 0.8037 (mp0) REVERT: E 157 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6507 (mtp85) REVERT: F 38 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: F 119 MET cc_start: 0.7822 (mmp) cc_final: 0.7448 (mmp) REVERT: G 46 GLU cc_start: 0.7947 (mp0) cc_final: 0.7239 (mp0) REVERT: G 150 GLU cc_start: 0.8768 (mp0) cc_final: 0.8037 (mp0) REVERT: G 157 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.6580 (mtp85) REVERT: H 38 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: H 119 MET cc_start: 0.7823 (mmp) cc_final: 0.7445 (mmp) outliers start: 66 outliers final: 50 residues processed: 244 average time/residue: 0.2366 time to fit residues: 81.3375 Evaluate side-chains 246 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 192 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11904 Z= 0.167 Angle : 0.559 7.547 16120 Z= 0.259 Chirality : 0.036 0.111 1840 Planarity : 0.005 0.050 1984 Dihedral : 3.502 10.806 1592 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 6.53 % Allowed : 15.33 % Favored : 78.14 % 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: 2.11 (0.22), residues: 1456 helix: 2.24 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.97 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 62 PHE 0.004 0.001 PHE H 197 TYR 0.013 0.001 TYR D 49 ARG 0.001 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 196 time to evaluate : 1.288 Fit side-chains REVERT: A 46 GLU cc_start: 0.7945 (mp0) cc_final: 0.7222 (mp0) REVERT: A 150 GLU cc_start: 0.8805 (mp0) cc_final: 0.7937 (mp0) REVERT: A 157 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6540 (mtp85) REVERT: B 38 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: B 104 GLN cc_start: 0.7202 (mp10) cc_final: 0.6975 (mp10) REVERT: B 119 MET cc_start: 0.7785 (mmp) cc_final: 0.7404 (mmp) REVERT: C 46 GLU cc_start: 0.7940 (mp0) cc_final: 0.7213 (mp0) REVERT: C 150 GLU cc_start: 0.8802 (mp0) cc_final: 0.7936 (mp0) REVERT: C 157 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.6538 (mtp85) REVERT: D 38 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: D 104 GLN cc_start: 0.7196 (mp10) cc_final: 0.6971 (mp10) REVERT: D 119 MET cc_start: 0.7781 (mmp) cc_final: 0.7406 (mmp) REVERT: E 46 GLU cc_start: 0.7940 (mp0) cc_final: 0.7218 (mp0) REVERT: E 150 GLU cc_start: 0.8804 (mp0) cc_final: 0.7936 (mp0) REVERT: E 157 ARG cc_start: 0.7275 (mtm-85) cc_final: 0.6462 (mtp85) REVERT: F 38 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: F 104 GLN cc_start: 0.7200 (mp10) cc_final: 0.6975 (mp10) REVERT: F 119 MET cc_start: 0.7790 (mmp) cc_final: 0.7414 (mmp) REVERT: G 46 GLU cc_start: 0.7940 (mp0) cc_final: 0.7215 (mp0) REVERT: G 150 GLU cc_start: 0.8803 (mp0) cc_final: 0.7935 (mp0) REVERT: G 157 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6461 (mtp85) REVERT: H 38 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: H 104 GLN cc_start: 0.7197 (mp10) cc_final: 0.6972 (mp10) REVERT: H 119 MET cc_start: 0.7790 (mmp) cc_final: 0.7415 (mmp) outliers start: 83 outliers final: 61 residues processed: 252 average time/residue: 0.2399 time to fit residues: 85.2979 Evaluate side-chains 261 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 0.3980 chunk 84 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11904 Z= 0.165 Angle : 0.570 7.528 16120 Z= 0.261 Chirality : 0.036 0.109 1840 Planarity : 0.005 0.050 1984 Dihedral : 3.484 10.638 1592 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 6.53 % Allowed : 15.80 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.22), residues: 1456 helix: 2.29 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.92 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 62 PHE 0.005 0.001 PHE D 154 TYR 0.009 0.001 TYR F 34 ARG 0.001 0.000 ARG F 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 206 time to evaluate : 1.276 Fit side-chains REVERT: A 46 GLU cc_start: 0.7948 (mp0) cc_final: 0.7239 (mp0) REVERT: A 150 GLU cc_start: 0.8772 (mp0) cc_final: 0.7962 (mp0) REVERT: A 157 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.6542 (mtp85) REVERT: B 38 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6662 (pm20) REVERT: B 119 MET cc_start: 0.7772 (mmp) cc_final: 0.7506 (mmp) REVERT: B 150 GLU cc_start: 0.8640 (mp0) cc_final: 0.8053 (mp0) REVERT: C 46 GLU cc_start: 0.7939 (mp0) cc_final: 0.7231 (mp0) REVERT: C 150 GLU cc_start: 0.8773 (mp0) cc_final: 0.7963 (mp0) REVERT: C 157 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.6541 (mtp85) REVERT: D 38 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: D 119 MET cc_start: 0.7772 (mmp) cc_final: 0.7499 (mmp) REVERT: D 150 GLU cc_start: 0.8640 (mp0) cc_final: 0.8052 (mp0) REVERT: E 46 GLU cc_start: 0.7943 (mp0) cc_final: 0.7233 (mp0) REVERT: E 150 GLU cc_start: 0.8774 (mp0) cc_final: 0.7962 (mp0) REVERT: E 157 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.6463 (mtp85) REVERT: F 38 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: F 119 MET cc_start: 0.7778 (mmp) cc_final: 0.7506 (mmp) REVERT: F 150 GLU cc_start: 0.8640 (mp0) cc_final: 0.8053 (mp0) REVERT: G 46 GLU cc_start: 0.7940 (mp0) cc_final: 0.7226 (mp0) REVERT: G 150 GLU cc_start: 0.8773 (mp0) cc_final: 0.7959 (mp0) REVERT: G 157 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6544 (mtp85) REVERT: H 38 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: H 119 MET cc_start: 0.7786 (mmp) cc_final: 0.7511 (mmp) REVERT: H 150 GLU cc_start: 0.8637 (mp0) cc_final: 0.8052 (mp0) outliers start: 83 outliers final: 64 residues processed: 258 average time/residue: 0.2379 time to fit residues: 86.3158 Evaluate side-chains 265 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11904 Z= 0.171 Angle : 0.571 7.504 16120 Z= 0.262 Chirality : 0.036 0.111 1840 Planarity : 0.005 0.050 1984 Dihedral : 3.481 10.621 1592 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.35 % Allowed : 16.90 % Favored : 77.75 % 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: 2.21 (0.22), residues: 1456 helix: 2.31 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.89 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 62 PHE 0.005 0.001 PHE F 154 TYR 0.015 0.001 TYR F 49 ARG 0.001 0.000 ARG G 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 1.304 Fit side-chains REVERT: A 46 GLU cc_start: 0.7942 (mp0) cc_final: 0.7238 (mp0) REVERT: A 150 GLU cc_start: 0.8617 (mp0) cc_final: 0.8201 (mp0) REVERT: A 157 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6522 (mtp85) REVERT: B 38 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: B 119 MET cc_start: 0.7771 (mmp) cc_final: 0.7475 (mmp) REVERT: C 46 GLU cc_start: 0.7930 (mp0) cc_final: 0.7223 (mp0) REVERT: C 150 GLU cc_start: 0.8618 (mp0) cc_final: 0.8201 (mp0) REVERT: C 157 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.6517 (mtp85) REVERT: D 38 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: D 119 MET cc_start: 0.7765 (mmp) cc_final: 0.7475 (mmp) REVERT: E 46 GLU cc_start: 0.7938 (mp0) cc_final: 0.7231 (mp0) REVERT: E 150 GLU cc_start: 0.8620 (mp0) cc_final: 0.8201 (mp0) REVERT: E 157 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6520 (mtp85) REVERT: F 38 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: F 119 MET cc_start: 0.7772 (mmp) cc_final: 0.7479 (mmp) REVERT: G 46 GLU cc_start: 0.7932 (mp0) cc_final: 0.7224 (mp0) REVERT: G 150 GLU cc_start: 0.8616 (mp0) cc_final: 0.8200 (mp0) REVERT: G 157 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6521 (mtp85) REVERT: H 38 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: H 119 MET cc_start: 0.7780 (mmp) cc_final: 0.7481 (mmp) outliers start: 68 outliers final: 64 residues processed: 248 average time/residue: 0.2465 time to fit residues: 85.6751 Evaluate side-chains 268 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 47 optimal weight: 0.0770 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.201260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.152010 restraints weight = 12479.700| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.76 r_work: 0.3432 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11904 Z= 0.161 Angle : 0.572 7.511 16120 Z= 0.261 Chirality : 0.036 0.136 1840 Planarity : 0.005 0.050 1984 Dihedral : 3.453 11.888 1592 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.50 % Allowed : 17.77 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.22), residues: 1456 helix: 2.37 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.85 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 62 PHE 0.004 0.001 PHE F 154 TYR 0.008 0.001 TYR C 176 ARG 0.001 0.000 ARG G 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.04 seconds wall clock time: 44 minutes 38.23 seconds (2678.23 seconds total)