Starting phenix.real_space_refine on Sat Mar 16 00:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/03_2024/6oks_20103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/03_2024/6oks_20103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/03_2024/6oks_20103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/03_2024/6oks_20103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/03_2024/6oks_20103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/03_2024/6oks_20103.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 56 5.16 5 C 8428 2.51 5 N 2184 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A ARG 868": "NH1" <-> "NH2" Residue "B TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B ARG 868": "NH1" <-> "NH2" Residue "C TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C ARG 868": "NH1" <-> "NH2" Residue "D TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 867": "OD1" <-> "OD2" Residue "D ARG 868": "NH1" <-> "NH2" Residue "E TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 867": "OD1" <-> "OD2" Residue "E ARG 868": "NH1" <-> "NH2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 867": "OD1" <-> "OD2" Residue "F ARG 868": "NH1" <-> "NH2" Residue "G TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 867": "OD1" <-> "OD2" Residue "G ARG 868": "NH1" <-> "NH2" Residue "H TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 867": "OD1" <-> "OD2" Residue "H ARG 868": "NH1" <-> "NH2" Residue "I TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 867": "OD1" <-> "OD2" Residue "I ARG 868": "NH1" <-> "NH2" Residue "J TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 867": "OD1" <-> "OD2" Residue "J ARG 868": "NH1" <-> "NH2" Residue "K TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 867": "OD1" <-> "OD2" Residue "K ARG 868": "NH1" <-> "NH2" Residue "L TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 867": "OD1" <-> "OD2" Residue "L ARG 868": "NH1" <-> "NH2" Residue "M TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 867": "OD1" <-> "OD2" Residue "M ARG 868": "NH1" <-> "NH2" Residue "N TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 867": "OD1" <-> "OD2" Residue "N ARG 868": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13244 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "B" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "G" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Time building chain proxies: 6.73, per 1000 atoms: 0.51 Number of scatterers: 13244 At special positions: 0 Unit cell: (126.15, 121.8, 89.9, 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 56 16.00 O 2576 8.00 N 2184 7.00 C 8428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.1 seconds 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 28 sheets defined 5.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.539A pdb=" N MET A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'E' and resid 759 through 764 Processing helix chain 'F' and resid 759 through 764 Processing helix chain 'G' and resid 759 through 764 Processing helix chain 'H' and resid 759 through 764 Processing helix chain 'I' and resid 759 through 764 Processing helix chain 'J' and resid 759 through 764 Processing helix chain 'K' and resid 759 through 764 Processing helix chain 'L' and resid 759 through 764 Processing helix chain 'M' and resid 759 through 764 Processing helix chain 'N' and resid 759 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY A 785 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN A 773 " --> pdb=" O ILE A 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE A 783 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP A 817 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA A 808 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 819 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 806 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU A 858 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY B 785 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN B 773 " --> pdb=" O ILE B 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE B 783 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP B 817 " --> pdb=" O ALA B 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA B 808 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 819 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 806 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 858 " --> pdb=" O GLU B 869 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY C 785 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN C 773 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE C 783 " --> pdb=" O ASN C 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP C 817 " --> pdb=" O ALA C 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA C 808 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 819 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 806 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU C 858 " --> pdb=" O GLU C 869 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY D 785 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN D 773 " --> pdb=" O ILE D 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 783 " --> pdb=" O ASN D 773 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP D 817 " --> pdb=" O ALA D 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA D 808 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY D 819 " --> pdb=" O VAL D 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 806 " --> pdb=" O GLY D 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU D 858 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY E 785 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN E 773 " --> pdb=" O ILE E 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE E 783 " --> pdb=" O ASN E 773 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP E 817 " --> pdb=" O ALA E 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA E 808 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY E 819 " --> pdb=" O VAL E 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL E 806 " --> pdb=" O GLY E 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU E 858 " --> pdb=" O GLU E 869 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY F 785 " --> pdb=" O ASP F 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN F 773 " --> pdb=" O ILE F 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE F 783 " --> pdb=" O ASN F 773 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP F 817 " --> pdb=" O ALA F 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA F 808 " --> pdb=" O ASP F 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY F 819 " --> pdb=" O VAL F 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 806 " --> pdb=" O GLY F 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU F 858 " --> pdb=" O GLU F 869 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY G 785 " --> pdb=" O ASP G 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN G 773 " --> pdb=" O ILE G 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE G 783 " --> pdb=" O ASN G 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP G 817 " --> pdb=" O ALA G 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA G 808 " --> pdb=" O ASP G 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY G 819 " --> pdb=" O VAL G 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 806 " --> pdb=" O GLY G 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU G 858 " --> pdb=" O GLU G 869 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY H 785 " --> pdb=" O ASP H 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN H 773 " --> pdb=" O ILE H 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE H 783 " --> pdb=" O ASN H 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP H 817 " --> pdb=" O ALA H 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA H 808 " --> pdb=" O ASP H 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY H 819 " --> pdb=" O VAL H 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 806 " --> pdb=" O GLY H 819 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU H 858 " --> pdb=" O GLU H 869 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY I 785 " --> pdb=" O ASP I 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN I 773 " --> pdb=" O ILE I 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE I 783 " --> pdb=" O ASN I 773 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP I 817 " --> pdb=" O ALA I 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA I 808 " --> pdb=" O ASP I 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY I 819 " --> pdb=" O VAL I 806 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 806 " --> pdb=" O GLY I 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU I 858 " --> pdb=" O GLU I 869 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY J 785 " --> pdb=" O ASP J 771 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN J 773 " --> pdb=" O ILE J 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE J 783 " --> pdb=" O ASN J 773 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP J 817 " --> pdb=" O ALA J 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA J 808 " --> pdb=" O ASP J 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY J 819 " --> pdb=" O VAL J 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL J 806 " --> pdb=" O GLY J 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU J 858 " --> pdb=" O GLU J 869 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY K 785 " --> pdb=" O ASP K 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN K 773 " --> pdb=" O ILE K 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE K 783 " --> pdb=" O ASN K 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP K 817 " --> pdb=" O ALA K 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA K 808 " --> pdb=" O ASP K 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY K 819 " --> pdb=" O VAL K 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL K 806 " --> pdb=" O GLY K 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU K 858 " --> pdb=" O GLU K 869 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY L 785 " --> pdb=" O ASP L 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN L 773 " --> pdb=" O ILE L 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE L 783 " --> pdb=" O ASN L 773 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP L 817 " --> pdb=" O ALA L 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA L 808 " --> pdb=" O ASP L 817 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY L 819 " --> pdb=" O VAL L 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL L 806 " --> pdb=" O GLY L 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU L 858 " --> pdb=" O GLU L 869 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY M 785 " --> pdb=" O ASP M 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN M 773 " --> pdb=" O ILE M 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE M 783 " --> pdb=" O ASN M 773 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP M 817 " --> pdb=" O ALA M 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA M 808 " --> pdb=" O ASP M 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY M 819 " --> pdb=" O VAL M 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL M 806 " --> pdb=" O GLY M 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU M 858 " --> pdb=" O GLU M 869 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY N 785 " --> pdb=" O ASP N 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN N 773 " --> pdb=" O ILE N 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE N 783 " --> pdb=" O ASN N 773 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP N 817 " --> pdb=" O ALA N 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA N 808 " --> pdb=" O ASP N 817 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY N 819 " --> pdb=" O VAL N 806 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL N 806 " --> pdb=" O GLY N 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU N 858 " --> pdb=" O GLU N 869 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 714 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: 2.81 Time building geometry restraints manager: 4.86 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: 4256 1.34 - 1.46: 2884 1.46 - 1.57: 6272 1.57 - 1.69: 14 1.69 - 1.81: 112 Bond restraints: 13538 Sorted by residual: bond pdb=" C ARG N 805 " pdb=" N VAL N 806 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.56e-02 4.11e+03 4.50e+00 bond pdb=" C ARG K 805 " pdb=" N VAL K 806 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.56e-02 4.11e+03 4.47e+00 bond pdb=" C ARG L 805 " pdb=" N VAL L 806 " ideal model delta sigma weight residual 1.330 1.298 0.033 1.56e-02 4.11e+03 4.42e+00 bond pdb=" C ARG G 805 " pdb=" N VAL G 806 " ideal model delta sigma weight residual 1.330 1.298 0.033 1.56e-02 4.11e+03 4.36e+00 bond pdb=" C ARG H 805 " pdb=" N VAL H 806 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.56e-02 4.11e+03 4.33e+00 ... (remaining 13533 not shown) Histogram of bond angle deviations from ideal: 100.68 - 106.84: 431 106.84 - 113.00: 6701 113.00 - 119.17: 3611 119.17 - 125.33: 7423 125.33 - 131.49: 132 Bond angle restraints: 18298 Sorted by residual: angle pdb=" CB GLU L 824 " pdb=" CG GLU L 824 " pdb=" CD GLU L 824 " ideal model delta sigma weight residual 112.60 121.58 -8.98 1.70e+00 3.46e-01 2.79e+01 angle pdb=" CB GLU C 824 " pdb=" CG GLU C 824 " pdb=" CD GLU C 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 angle pdb=" CB GLU A 824 " pdb=" CG GLU A 824 " pdb=" CD GLU A 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 angle pdb=" CB GLU N 824 " pdb=" CG GLU N 824 " pdb=" CD GLU N 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 angle pdb=" CB GLU I 824 " pdb=" CG GLU I 824 " pdb=" CD GLU I 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 ... (remaining 18293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 6664 13.87 - 27.75: 915 27.75 - 41.62: 317 41.62 - 55.49: 196 55.49 - 69.36: 56 Dihedral angle restraints: 8148 sinusoidal: 3374 harmonic: 4774 Sorted by residual: dihedral pdb=" CA TYR K 861 " pdb=" C TYR K 861 " pdb=" N ALA K 862 " pdb=" CA ALA K 862 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASP F 758 " pdb=" C ASP F 758 " pdb=" N GLN F 759 " pdb=" CA GLN F 759 " ideal model delta harmonic sigma weight residual -180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TYR D 861 " pdb=" C TYR D 861 " pdb=" N ALA D 862 " pdb=" CA ALA D 862 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 8145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1061 0.036 - 0.072: 526 0.072 - 0.108: 192 0.108 - 0.144: 125 0.144 - 0.180: 14 Chirality restraints: 1918 Sorted by residual: chirality pdb=" CB ILE D 801 " pdb=" CA ILE D 801 " pdb=" CG1 ILE D 801 " pdb=" CG2 ILE D 801 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CB ILE E 801 " pdb=" CA ILE E 801 " pdb=" CG1 ILE E 801 " pdb=" CG2 ILE E 801 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CB ILE H 801 " pdb=" CA ILE H 801 " pdb=" CG1 ILE H 801 " pdb=" CG2 ILE H 801 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1915 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 864 " -0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO E 865 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 865 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 865 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 864 " -0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO M 865 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO M 865 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 865 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 864 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO F 865 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 865 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 865 " -0.045 5.00e-02 4.00e+02 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4200 2.82 - 3.34: 10897 3.34 - 3.86: 21318 3.86 - 4.38: 22480 4.38 - 4.90: 38628 Nonbonded interactions: 97523 Sorted by model distance: nonbonded pdb=" NE2 HIS M 765 " pdb=" OE2 GLU M 869 " model vdw 2.299 2.520 nonbonded pdb=" NE2 HIS G 765 " pdb=" OE2 GLU G 869 " model vdw 2.299 2.520 nonbonded pdb=" NE2 HIS A 765 " pdb=" OE2 GLU A 869 " model vdw 2.299 2.520 nonbonded pdb=" NE2 HIS K 765 " pdb=" OE2 GLU K 869 " model vdw 2.299 2.520 nonbonded pdb=" NE2 HIS B 765 " pdb=" OE2 GLU B 869 " model vdw 2.299 2.520 ... (remaining 97518 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.020 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.720 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.008 0.055 13538 Z= 0.516 Angle : 1.152 10.178 18298 Z= 0.655 Chirality : 0.053 0.180 1918 Planarity : 0.009 0.079 2394 Dihedral : 17.363 69.364 5124 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 9.80 % Allowed : 6.86 % Favored : 83.33 % 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: -5.50 (0.15), residues: 1582 helix: -4.78 (0.17), residues: 182 sheet: -2.21 (0.36), residues: 168 loop : -4.08 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS H 765 PHE 0.015 0.002 PHE M 774 TYR 0.018 0.002 TYR I 855 ARG 0.009 0.001 ARG G 868 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 534 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 762 MET cc_start: 0.6611 (mtt) cc_final: 0.6090 (mtt) REVERT: A 780 ASN cc_start: 0.8567 (p0) cc_final: 0.8007 (p0) REVERT: A 791 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8417 (p) REVERT: B 759 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 762 MET cc_start: 0.6854 (mtt) cc_final: 0.6564 (mtt) REVERT: B 780 ASN cc_start: 0.8224 (p0) cc_final: 0.7846 (p0) REVERT: B 786 MET cc_start: 0.8440 (tpp) cc_final: 0.7776 (ttt) REVERT: B 787 TYR cc_start: 0.8594 (m-10) cc_final: 0.8301 (m-80) REVERT: B 791 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8398 (p) REVERT: B 806 VAL cc_start: 0.9660 (OUTLIER) cc_final: 0.9301 (m) REVERT: C 759 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 762 MET cc_start: 0.7033 (mtt) cc_final: 0.6508 (mtt) REVERT: C 786 MET cc_start: 0.8143 (tpp) cc_final: 0.7636 (tpp) REVERT: C 787 TYR cc_start: 0.8445 (m-10) cc_final: 0.8078 (m-80) REVERT: C 791 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8556 (p) REVERT: C 800 TYR cc_start: 0.8400 (t80) cc_final: 0.8142 (t80) REVERT: C 868 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7577 (mmt90) REVERT: D 759 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8349 (tm-30) REVERT: D 762 MET cc_start: 0.7067 (mtt) cc_final: 0.6475 (mtt) REVERT: D 780 ASN cc_start: 0.9094 (p0) cc_final: 0.8758 (p0) REVERT: D 786 MET cc_start: 0.8292 (tpp) cc_final: 0.7923 (tpp) REVERT: D 787 TYR cc_start: 0.8377 (m-10) cc_final: 0.7858 (m-80) REVERT: D 791 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 824 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: D 825 MET cc_start: 0.8144 (mtp) cc_final: 0.7780 (mtp) REVERT: E 762 MET cc_start: 0.7253 (mtt) cc_final: 0.6834 (mtt) REVERT: E 787 TYR cc_start: 0.8514 (m-10) cc_final: 0.8214 (m-10) REVERT: E 791 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 800 TYR cc_start: 0.8598 (t80) cc_final: 0.8358 (t80) REVERT: E 806 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9204 (m) REVERT: E 824 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: F 762 MET cc_start: 0.6846 (mtt) cc_final: 0.6603 (mtt) REVERT: F 780 ASN cc_start: 0.8416 (p0) cc_final: 0.7943 (p0) REVERT: F 787 TYR cc_start: 0.8728 (m-10) cc_final: 0.8203 (m-10) REVERT: F 791 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8404 (p) REVERT: G 759 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8679 (tm-30) REVERT: G 762 MET cc_start: 0.7170 (mtt) cc_final: 0.6378 (mtt) REVERT: G 780 ASN cc_start: 0.8335 (p0) cc_final: 0.8091 (p0) REVERT: G 787 TYR cc_start: 0.8640 (m-10) cc_final: 0.8322 (m-10) REVERT: G 791 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8734 (p) REVERT: G 868 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7519 (mmt180) REVERT: H 790 PRO cc_start: 0.6800 (Cg_endo) cc_final: 0.6541 (Cg_exo) REVERT: H 791 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8230 (m) REVERT: H 807 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6889 (mm-30) REVERT: H 824 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: H 856 LYS cc_start: 0.8508 (tmmt) cc_final: 0.7903 (tmtt) REVERT: H 870 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9039 (tt) REVERT: I 762 MET cc_start: 0.6732 (mtt) cc_final: 0.6353 (mtt) REVERT: I 803 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7777 (mtpp) REVERT: I 824 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: I 852 ILE cc_start: 0.8398 (pt) cc_final: 0.8177 (tp) REVERT: I 856 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8107 (tmtt) REVERT: I 870 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9028 (tt) REVERT: J 762 MET cc_start: 0.7206 (mtt) cc_final: 0.6855 (mtt) REVERT: J 786 MET cc_start: 0.8131 (tpp) cc_final: 0.7837 (mmm) REVERT: J 807 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6544 (mm-30) REVERT: J 870 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9105 (tt) REVERT: K 791 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8547 (m) REVERT: L 783 ILE cc_start: 0.9444 (mt) cc_final: 0.8902 (mt) REVERT: L 786 MET cc_start: 0.7982 (tpp) cc_final: 0.7531 (mmm) REVERT: L 824 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: L 856 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7347 (tmtt) REVERT: L 859 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6106 (mmm-85) REVERT: L 866 ASP cc_start: 0.8868 (m-30) cc_final: 0.8365 (m-30) REVERT: M 762 MET cc_start: 0.7227 (mtt) cc_final: 0.6853 (mtt) REVERT: M 783 ILE cc_start: 0.9622 (mt) cc_final: 0.8744 (mp) REVERT: M 786 MET cc_start: 0.8053 (tpp) cc_final: 0.7604 (mmm) REVERT: M 807 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6815 (mm-30) REVERT: M 852 ILE cc_start: 0.8282 (pt) cc_final: 0.7925 (tp) REVERT: N 762 MET cc_start: 0.7389 (mtt) cc_final: 0.7166 (mtt) REVERT: N 806 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8767 (t) REVERT: N 807 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6161 (mm-30) REVERT: N 824 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: N 856 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7897 (ttpp) outliers start: 140 outliers final: 25 residues processed: 589 average time/residue: 0.2464 time to fit residues: 204.7606 Evaluate side-chains 374 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 328 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.0020 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 851 ASN ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13538 Z= 0.177 Angle : 0.676 6.410 18298 Z= 0.349 Chirality : 0.042 0.176 1918 Planarity : 0.006 0.068 2394 Dihedral : 6.546 23.813 1820 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -5.42 (0.15), residues: 1582 helix: -4.23 (0.22), residues: 168 sheet: -2.15 (0.38), residues: 168 loop : -4.12 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 765 PHE 0.010 0.001 PHE I 788 TYR 0.016 0.001 TYR F 800 ARG 0.004 0.000 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 762 MET cc_start: 0.5872 (mtt) cc_final: 0.5652 (mtt) REVERT: A 780 ASN cc_start: 0.8298 (p0) cc_final: 0.7582 (p0) REVERT: A 800 TYR cc_start: 0.8481 (t80) cc_final: 0.7909 (t80) REVERT: B 759 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8529 (pm20) REVERT: B 780 ASN cc_start: 0.8074 (p0) cc_final: 0.7498 (p0) REVERT: B 786 MET cc_start: 0.8317 (tpp) cc_final: 0.7632 (ttt) REVERT: B 800 TYR cc_start: 0.8212 (t80) cc_final: 0.7913 (t80) REVERT: C 762 MET cc_start: 0.6710 (mtt) cc_final: 0.6201 (mtt) REVERT: C 800 TYR cc_start: 0.8310 (t80) cc_final: 0.8019 (t80) REVERT: C 858 LEU cc_start: 0.8703 (tp) cc_final: 0.8255 (tp) REVERT: C 866 ASP cc_start: 0.8757 (m-30) cc_final: 0.8555 (m-30) REVERT: D 759 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 762 MET cc_start: 0.6517 (mtt) cc_final: 0.5985 (mtt) REVERT: D 780 ASN cc_start: 0.8455 (p0) cc_final: 0.8208 (p0) REVERT: D 791 THR cc_start: 0.8172 (p) cc_final: 0.7914 (p) REVERT: D 800 TYR cc_start: 0.8199 (t80) cc_final: 0.7667 (t80) REVERT: D 817 ASP cc_start: 0.7128 (t70) cc_final: 0.6914 (t0) REVERT: E 762 MET cc_start: 0.7091 (mtt) cc_final: 0.6724 (mtt) REVERT: E 786 MET cc_start: 0.8327 (tpp) cc_final: 0.7992 (tpp) REVERT: E 791 THR cc_start: 0.8168 (p) cc_final: 0.7909 (p) REVERT: E 800 TYR cc_start: 0.8779 (t80) cc_final: 0.8557 (t80) REVERT: E 866 ASP cc_start: 0.8795 (m-30) cc_final: 0.7827 (t0) REVERT: F 762 MET cc_start: 0.5694 (mtt) cc_final: 0.5468 (mtt) REVERT: F 780 ASN cc_start: 0.8105 (p0) cc_final: 0.7745 (p0) REVERT: F 791 THR cc_start: 0.8154 (p) cc_final: 0.7889 (p) REVERT: F 806 VAL cc_start: 0.9444 (m) cc_final: 0.9170 (p) REVERT: F 807 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7958 (mm-30) REVERT: F 816 LYS cc_start: 0.9064 (pptt) cc_final: 0.8832 (pptt) REVERT: F 856 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8201 (tmtt) REVERT: G 759 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8570 (tm-30) REVERT: G 762 MET cc_start: 0.6182 (mtt) cc_final: 0.5631 (mtt) REVERT: G 780 ASN cc_start: 0.8149 (p0) cc_final: 0.7559 (p0) REVERT: G 800 TYR cc_start: 0.8713 (t80) cc_final: 0.8481 (t80) REVERT: G 803 LYS cc_start: 0.8702 (mttt) cc_final: 0.8452 (mttm) REVERT: G 868 ARG cc_start: 0.7668 (mtt-85) cc_final: 0.7342 (mmt90) REVERT: H 771 ASP cc_start: 0.8735 (t0) cc_final: 0.7060 (p0) REVERT: H 807 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6940 (mm-30) REVERT: H 825 MET cc_start: 0.8383 (mtm) cc_final: 0.8161 (pmm) REVERT: H 856 LYS cc_start: 0.8338 (tmmt) cc_final: 0.8133 (tmtt) REVERT: I 782 TYR cc_start: 0.7636 (m-80) cc_final: 0.7231 (m-80) REVERT: I 807 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6464 (mm-30) REVERT: I 852 ILE cc_start: 0.8413 (pt) cc_final: 0.8101 (tp) REVERT: I 856 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8193 (tmtt) REVERT: I 870 LEU cc_start: 0.9398 (tp) cc_final: 0.9137 (tt) REVERT: J 762 MET cc_start: 0.7214 (mtt) cc_final: 0.6813 (mtt) REVERT: J 786 MET cc_start: 0.8241 (tpp) cc_final: 0.7934 (tmm) REVERT: J 807 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6793 (mm-30) REVERT: J 870 LEU cc_start: 0.9180 (tp) cc_final: 0.8870 (tt) REVERT: K 762 MET cc_start: 0.8227 (mtm) cc_final: 0.7651 (mtt) REVERT: K 771 ASP cc_start: 0.8897 (t0) cc_final: 0.7662 (p0) REVERT: K 772 LEU cc_start: 0.9167 (mp) cc_final: 0.8913 (mp) REVERT: K 782 TYR cc_start: 0.8142 (m-80) cc_final: 0.7715 (m-80) REVERT: K 836 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7806 (mmmm) REVERT: L 786 MET cc_start: 0.8300 (tpp) cc_final: 0.7927 (mmm) REVERT: L 813 SER cc_start: 0.6787 (t) cc_final: 0.6457 (p) REVERT: L 858 LEU cc_start: 0.8372 (tp) cc_final: 0.7547 (tp) REVERT: L 859 ARG cc_start: 0.7291 (mmm-85) cc_final: 0.6786 (mtp85) REVERT: M 807 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6192 (mm-30) REVERT: M 825 MET cc_start: 0.8297 (pmm) cc_final: 0.8041 (ptm) REVERT: M 852 ILE cc_start: 0.8291 (pt) cc_final: 0.8072 (tp) REVERT: M 870 LEU cc_start: 0.9455 (tt) cc_final: 0.9243 (tt) REVERT: N 762 MET cc_start: 0.7268 (mtt) cc_final: 0.6830 (mtt) REVERT: N 771 ASP cc_start: 0.8738 (t0) cc_final: 0.7181 (p0) REVERT: N 807 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6160 (mm-30) REVERT: N 825 MET cc_start: 0.8408 (ptp) cc_final: 0.7919 (ptp) REVERT: N 855 TYR cc_start: 0.6841 (m-10) cc_final: 0.6594 (m-80) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.2461 time to fit residues: 162.2814 Evaluate side-chains 349 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 851 ASN ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13538 Z= 0.314 Angle : 0.761 6.907 18298 Z= 0.398 Chirality : 0.043 0.158 1918 Planarity : 0.007 0.071 2394 Dihedral : 6.577 21.229 1820 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.31 % Favored : 83.69 % Rotamer: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.89 % 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: -5.40 (0.15), residues: 1582 helix: -4.12 (0.22), residues: 182 sheet: -1.83 (0.39), residues: 168 loop : -4.16 (0.12), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 765 PHE 0.015 0.002 PHE E 774 TYR 0.020 0.002 TYR N 855 ARG 0.007 0.001 ARG E 859 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 762 MET cc_start: 0.6414 (mtt) cc_final: 0.5970 (mtt) REVERT: A 780 ASN cc_start: 0.8360 (p0) cc_final: 0.7943 (p0) REVERT: A 853 MET cc_start: 0.8063 (ppp) cc_final: 0.7838 (ppp) REVERT: A 856 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8336 (tmtt) REVERT: A 870 LEU cc_start: 0.9653 (tp) cc_final: 0.9181 (tp) REVERT: B 780 ASN cc_start: 0.7971 (p0) cc_final: 0.7625 (p0) REVERT: B 786 MET cc_start: 0.8329 (tpp) cc_final: 0.7970 (ttt) REVERT: B 787 TYR cc_start: 0.8820 (m-10) cc_final: 0.8462 (m-80) REVERT: B 800 TYR cc_start: 0.8445 (t80) cc_final: 0.8232 (t80) REVERT: B 807 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7993 (mm-30) REVERT: C 762 MET cc_start: 0.6958 (mtt) cc_final: 0.6061 (mtt) REVERT: C 786 MET cc_start: 0.8289 (tpp) cc_final: 0.8034 (tpp) REVERT: C 800 TYR cc_start: 0.8505 (t80) cc_final: 0.8241 (t80) REVERT: C 807 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8171 (mm-30) REVERT: D 759 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 762 MET cc_start: 0.7144 (mtt) cc_final: 0.6478 (mtt) REVERT: D 780 ASN cc_start: 0.8800 (p0) cc_final: 0.8212 (p0) REVERT: D 786 MET cc_start: 0.8240 (tpp) cc_final: 0.7846 (tpt) REVERT: D 787 TYR cc_start: 0.8693 (m-10) cc_final: 0.8403 (m-80) REVERT: D 791 THR cc_start: 0.8432 (p) cc_final: 0.8179 (p) REVERT: D 800 TYR cc_start: 0.8398 (t80) cc_final: 0.8139 (t80) REVERT: E 762 MET cc_start: 0.7210 (mtt) cc_final: 0.6845 (mtt) REVERT: E 786 MET cc_start: 0.7962 (tpp) cc_final: 0.7640 (tpp) REVERT: E 787 TYR cc_start: 0.8914 (m-10) cc_final: 0.8625 (m-80) REVERT: E 791 THR cc_start: 0.8472 (p) cc_final: 0.8233 (p) REVERT: E 800 TYR cc_start: 0.8836 (t80) cc_final: 0.8550 (t80) REVERT: E 824 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7580 (tm-30) REVERT: E 866 ASP cc_start: 0.8795 (m-30) cc_final: 0.8099 (t0) REVERT: F 762 MET cc_start: 0.6560 (mtt) cc_final: 0.5934 (mtt) REVERT: F 780 ASN cc_start: 0.8228 (p0) cc_final: 0.7914 (p0) REVERT: F 787 TYR cc_start: 0.8679 (m-80) cc_final: 0.8024 (m-80) REVERT: F 791 THR cc_start: 0.8677 (p) cc_final: 0.8437 (p) REVERT: F 806 VAL cc_start: 0.9610 (m) cc_final: 0.9299 (p) REVERT: F 807 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8104 (mm-30) REVERT: F 824 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7629 (tm-30) REVERT: F 825 MET cc_start: 0.8028 (mtt) cc_final: 0.7663 (mtt) REVERT: F 850 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7536 (mt-10) REVERT: G 759 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8606 (tm-30) REVERT: G 762 MET cc_start: 0.6654 (mtt) cc_final: 0.6014 (mtt) REVERT: G 772 LEU cc_start: 0.9511 (mt) cc_final: 0.9271 (mm) REVERT: G 780 ASN cc_start: 0.8382 (p0) cc_final: 0.7830 (p0) REVERT: G 787 TYR cc_start: 0.8943 (m-10) cc_final: 0.8426 (m-80) REVERT: G 803 LYS cc_start: 0.8690 (mttt) cc_final: 0.8417 (mttm) REVERT: G 853 MET cc_start: 0.7905 (ppp) cc_final: 0.7536 (ppp) REVERT: H 771 ASP cc_start: 0.8861 (t0) cc_final: 0.6938 (p0) REVERT: H 772 LEU cc_start: 0.9327 (mp) cc_final: 0.9092 (mp) REVERT: H 807 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6977 (mm-30) REVERT: H 824 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7187 (tm-30) REVERT: H 868 ARG cc_start: 0.8277 (mmt180) cc_final: 0.7963 (mmm-85) REVERT: I 762 MET cc_start: 0.8126 (mtm) cc_final: 0.7713 (mtt) REVERT: I 807 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6327 (mm-30) REVERT: I 856 LYS cc_start: 0.9042 (tmmt) cc_final: 0.8547 (tttm) REVERT: I 870 LEU cc_start: 0.9375 (tp) cc_final: 0.8902 (tt) REVERT: J 762 MET cc_start: 0.7289 (mtt) cc_final: 0.6742 (mtt) REVERT: J 787 TYR cc_start: 0.8245 (m-80) cc_final: 0.8000 (m-80) REVERT: J 807 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6675 (mm-30) REVERT: J 855 TYR cc_start: 0.6315 (m-10) cc_final: 0.6069 (m-80) REVERT: J 866 ASP cc_start: 0.8952 (m-30) cc_final: 0.8691 (m-30) REVERT: J 868 ARG cc_start: 0.8285 (mmt180) cc_final: 0.7678 (mmm-85) REVERT: J 870 LEU cc_start: 0.9020 (tp) cc_final: 0.8592 (tt) REVERT: K 771 ASP cc_start: 0.9035 (t0) cc_final: 0.7458 (p0) REVERT: K 772 LEU cc_start: 0.9322 (mp) cc_final: 0.8925 (mp) REVERT: K 870 LEU cc_start: 0.9210 (tt) cc_final: 0.8943 (tt) REVERT: L 771 ASP cc_start: 0.8890 (t0) cc_final: 0.6945 (p0) REVERT: L 772 LEU cc_start: 0.9372 (mp) cc_final: 0.9014 (mp) REVERT: L 786 MET cc_start: 0.8101 (tpp) cc_final: 0.7608 (mmm) REVERT: L 807 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6734 (mm-30) REVERT: L 813 SER cc_start: 0.6954 (t) cc_final: 0.6693 (p) REVERT: M 762 MET cc_start: 0.8168 (mtm) cc_final: 0.7942 (mtt) REVERT: M 771 ASP cc_start: 0.9036 (t0) cc_final: 0.7475 (p0) REVERT: M 786 MET cc_start: 0.8773 (tpp) cc_final: 0.8482 (tpp) REVERT: M 807 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6427 (mm-30) REVERT: M 825 MET cc_start: 0.8351 (pmm) cc_final: 0.8139 (pmm) REVERT: M 852 ILE cc_start: 0.8389 (pt) cc_final: 0.8188 (tp) REVERT: N 762 MET cc_start: 0.7237 (mtt) cc_final: 0.6743 (mtt) REVERT: N 771 ASP cc_start: 0.8959 (t0) cc_final: 0.7255 (p0) REVERT: N 772 LEU cc_start: 0.9430 (mp) cc_final: 0.9197 (mp) REVERT: N 807 GLU cc_start: 0.7252 (mt-10) cc_final: 0.5842 (mm-30) REVERT: N 824 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7800 (tm-30) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.2326 time to fit residues: 132.2714 Evaluate side-chains 313 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13538 Z= 0.361 Angle : 0.787 7.310 18298 Z= 0.411 Chirality : 0.044 0.142 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.828 23.191 1820 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.02 % Favored : 81.98 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.15), residues: 1582 helix: -3.80 (0.24), residues: 182 sheet: -1.73 (0.39), residues: 168 loop : -4.12 (0.12), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS G 765 PHE 0.015 0.002 PHE G 774 TYR 0.019 0.002 TYR K 855 ARG 0.011 0.001 ARG L 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 MET cc_start: 0.6633 (mtt) cc_final: 0.6117 (mtt) REVERT: A 870 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (tp) REVERT: B 780 ASN cc_start: 0.8291 (p0) cc_final: 0.7950 (p0) REVERT: B 786 MET cc_start: 0.8498 (tpp) cc_final: 0.8162 (ttt) REVERT: B 800 TYR cc_start: 0.8584 (t80) cc_final: 0.8341 (t80) REVERT: B 803 LYS cc_start: 0.8833 (mttt) cc_final: 0.8579 (mttm) REVERT: B 807 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 824 GLU cc_start: 0.8886 (tp30) cc_final: 0.8005 (tm-30) REVERT: B 829 LEU cc_start: 0.9535 (mt) cc_final: 0.9095 (mt) REVERT: B 856 LYS cc_start: 0.8867 (tmtt) cc_final: 0.8409 (tmtt) REVERT: C 759 GLN cc_start: 0.8962 (pm20) cc_final: 0.8738 (pm20) REVERT: C 762 MET cc_start: 0.7291 (mtt) cc_final: 0.6434 (mtt) REVERT: C 786 MET cc_start: 0.8237 (tpp) cc_final: 0.7924 (tpp) REVERT: D 759 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 762 MET cc_start: 0.7315 (mtt) cc_final: 0.6572 (mtt) REVERT: D 780 ASN cc_start: 0.8783 (p0) cc_final: 0.8152 (p0) REVERT: D 786 MET cc_start: 0.8383 (tpp) cc_final: 0.8067 (tpt) REVERT: D 787 TYR cc_start: 0.8900 (m-10) cc_final: 0.8257 (m-80) REVERT: D 791 THR cc_start: 0.8536 (p) cc_final: 0.8303 (p) REVERT: D 800 TYR cc_start: 0.8430 (t80) cc_final: 0.8196 (t80) REVERT: D 851 ASN cc_start: 0.7848 (t0) cc_final: 0.7587 (t0) REVERT: D 856 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8380 (ttpp) REVERT: E 762 MET cc_start: 0.7372 (mtt) cc_final: 0.6869 (mtt) REVERT: E 787 TYR cc_start: 0.9059 (m-10) cc_final: 0.8476 (m-80) REVERT: E 791 THR cc_start: 0.8638 (p) cc_final: 0.8384 (p) REVERT: E 800 TYR cc_start: 0.8852 (t80) cc_final: 0.8409 (t80) REVERT: E 824 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7969 (tm-30) REVERT: E 860 ILE cc_start: 0.8646 (mm) cc_final: 0.8439 (mm) REVERT: E 866 ASP cc_start: 0.8807 (m-30) cc_final: 0.8033 (t0) REVERT: F 762 MET cc_start: 0.6829 (mtt) cc_final: 0.6515 (mtt) REVERT: F 780 ASN cc_start: 0.8376 (p0) cc_final: 0.8022 (p0) REVERT: F 806 VAL cc_start: 0.9678 (m) cc_final: 0.9364 (p) REVERT: F 807 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8176 (mm-30) REVERT: F 816 LYS cc_start: 0.9128 (pptt) cc_final: 0.8886 (ptmt) REVERT: F 824 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8001 (tm-30) REVERT: F 850 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7342 (mt-10) REVERT: F 856 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8414 (tmtt) REVERT: G 759 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8625 (tm-30) REVERT: G 762 MET cc_start: 0.7068 (mtt) cc_final: 0.6303 (mtt) REVERT: G 772 LEU cc_start: 0.9548 (mt) cc_final: 0.9253 (mm) REVERT: G 780 ASN cc_start: 0.8363 (p0) cc_final: 0.7912 (p0) REVERT: G 787 TYR cc_start: 0.9110 (m-10) cc_final: 0.8835 (m-10) REVERT: G 803 LYS cc_start: 0.8721 (mttt) cc_final: 0.8444 (mttm) REVERT: G 853 MET cc_start: 0.7623 (ppp) cc_final: 0.7401 (ppp) REVERT: H 771 ASP cc_start: 0.8966 (t0) cc_final: 0.6924 (p0) REVERT: H 772 LEU cc_start: 0.9412 (mp) cc_final: 0.9122 (mp) REVERT: H 807 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6099 (tm-30) REVERT: H 824 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7562 (tm-30) REVERT: H 825 MET cc_start: 0.8604 (pmm) cc_final: 0.8329 (pmm) REVERT: I 762 MET cc_start: 0.8247 (mtm) cc_final: 0.7938 (mtt) REVERT: I 807 GLU cc_start: 0.7172 (mt-10) cc_final: 0.5933 (tm-30) REVERT: I 817 ASP cc_start: 0.8844 (t70) cc_final: 0.8606 (t0) REVERT: I 825 MET cc_start: 0.8461 (pmm) cc_final: 0.8253 (pmm) REVERT: I 856 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8590 (tttm) REVERT: I 866 ASP cc_start: 0.8715 (m-30) cc_final: 0.8501 (m-30) REVERT: I 870 LEU cc_start: 0.9363 (tp) cc_final: 0.9015 (tt) REVERT: J 762 MET cc_start: 0.7409 (mtt) cc_final: 0.6920 (mtt) REVERT: J 807 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6523 (tm-30) REVERT: J 824 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8167 (tm-30) REVERT: J 870 LEU cc_start: 0.9014 (tp) cc_final: 0.8600 (tt) REVERT: K 762 MET cc_start: 0.8187 (mtm) cc_final: 0.7756 (mtt) REVERT: L 771 ASP cc_start: 0.8987 (t0) cc_final: 0.6899 (p0) REVERT: L 772 LEU cc_start: 0.9449 (mp) cc_final: 0.9069 (mp) REVERT: L 786 MET cc_start: 0.8006 (tpp) cc_final: 0.7553 (mmm) REVERT: L 807 GLU cc_start: 0.7260 (mt-10) cc_final: 0.5660 (tm-30) REVERT: L 824 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7806 (tm-30) REVERT: L 866 ASP cc_start: 0.8646 (m-30) cc_final: 0.8438 (m-30) REVERT: M 762 MET cc_start: 0.8203 (mtm) cc_final: 0.7884 (mtt) REVERT: M 771 ASP cc_start: 0.9110 (t0) cc_final: 0.7616 (p0) REVERT: M 786 MET cc_start: 0.8840 (tpp) cc_final: 0.8542 (tpp) REVERT: M 807 GLU cc_start: 0.7255 (mt-10) cc_final: 0.5973 (tm-30) REVERT: M 824 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8080 (tm-30) REVERT: M 858 LEU cc_start: 0.8178 (tp) cc_final: 0.7749 (tp) REVERT: N 762 MET cc_start: 0.7334 (mtt) cc_final: 0.6802 (mtt) REVERT: N 771 ASP cc_start: 0.8998 (t0) cc_final: 0.7038 (p0) REVERT: N 772 LEU cc_start: 0.9503 (mp) cc_final: 0.9236 (mp) REVERT: N 807 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6315 (tm-30) REVERT: N 824 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7897 (tm-30) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.2418 time to fit residues: 137.5710 Evaluate side-chains 308 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 838 ASN ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 765 HIS L 765 HIS ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13538 Z= 0.275 Angle : 0.732 7.793 18298 Z= 0.380 Chirality : 0.044 0.148 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.519 22.694 1820 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -5.39 (0.16), residues: 1582 helix: -3.42 (0.28), residues: 182 sheet: -3.24 (0.26), residues: 308 loop : -4.01 (0.14), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 765 PHE 0.012 0.001 PHE M 788 TYR 0.017 0.001 TYR D 861 ARG 0.009 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 MET cc_start: 0.6797 (mtt) cc_final: 0.6271 (mtt) REVERT: A 824 GLU cc_start: 0.9028 (tp30) cc_final: 0.7821 (tm-30) REVERT: A 825 MET cc_start: 0.7971 (mtt) cc_final: 0.7760 (mtt) REVERT: A 853 MET cc_start: 0.8163 (ppp) cc_final: 0.7937 (ppp) REVERT: A 860 ILE cc_start: 0.8363 (mp) cc_final: 0.6962 (mp) REVERT: A 869 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 870 LEU cc_start: 0.9653 (tp) cc_final: 0.9442 (tp) REVERT: B 780 ASN cc_start: 0.8252 (p0) cc_final: 0.7836 (p0) REVERT: B 786 MET cc_start: 0.8372 (tpp) cc_final: 0.8114 (ttt) REVERT: B 787 TYR cc_start: 0.8768 (m-10) cc_final: 0.8537 (m-10) REVERT: B 800 TYR cc_start: 0.8609 (t80) cc_final: 0.8319 (t80) REVERT: B 803 LYS cc_start: 0.8797 (mttt) cc_final: 0.8499 (mttm) REVERT: B 807 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8390 (mm-30) REVERT: B 824 GLU cc_start: 0.8861 (tp30) cc_final: 0.7988 (tm-30) REVERT: B 829 LEU cc_start: 0.9534 (mt) cc_final: 0.9139 (mt) REVERT: C 762 MET cc_start: 0.7314 (mtt) cc_final: 0.6398 (mtt) REVERT: C 786 MET cc_start: 0.8334 (tpp) cc_final: 0.8001 (tpp) REVERT: C 825 MET cc_start: 0.8567 (tpt) cc_final: 0.7968 (tpt) REVERT: C 866 ASP cc_start: 0.8558 (m-30) cc_final: 0.7825 (t0) REVERT: D 759 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8337 (tm-30) REVERT: D 762 MET cc_start: 0.7094 (mtt) cc_final: 0.6503 (mtt) REVERT: D 780 ASN cc_start: 0.8739 (p0) cc_final: 0.8091 (p0) REVERT: D 786 MET cc_start: 0.8291 (tpp) cc_final: 0.7940 (tpt) REVERT: D 791 THR cc_start: 0.8433 (p) cc_final: 0.8198 (p) REVERT: D 800 TYR cc_start: 0.8351 (t80) cc_final: 0.8095 (t80) REVERT: D 851 ASN cc_start: 0.7822 (t0) cc_final: 0.7549 (t0) REVERT: E 762 MET cc_start: 0.7364 (mtt) cc_final: 0.6857 (mtt) REVERT: E 787 TYR cc_start: 0.8952 (m-10) cc_final: 0.8695 (m-80) REVERT: E 791 THR cc_start: 0.8548 (p) cc_final: 0.8308 (p) REVERT: E 800 TYR cc_start: 0.8745 (t80) cc_final: 0.8439 (t80) REVERT: E 824 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7932 (tm-30) REVERT: E 825 MET cc_start: 0.8219 (tpp) cc_final: 0.7988 (tpt) REVERT: E 829 LEU cc_start: 0.9524 (mt) cc_final: 0.9252 (mt) REVERT: E 866 ASP cc_start: 0.8848 (m-30) cc_final: 0.8069 (t0) REVERT: F 759 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 762 MET cc_start: 0.6984 (mtt) cc_final: 0.6545 (mtt) REVERT: F 807 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8174 (mm-30) REVERT: F 816 LYS cc_start: 0.9003 (pptt) cc_final: 0.8796 (ptmt) REVERT: F 824 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8041 (tm-30) REVERT: F 825 MET cc_start: 0.8033 (mtt) cc_final: 0.7240 (mtt) REVERT: F 850 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7318 (mt-10) REVERT: F 856 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8304 (tmtt) REVERT: G 759 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8659 (tm-30) REVERT: G 762 MET cc_start: 0.6888 (mtt) cc_final: 0.6109 (mtt) REVERT: G 772 LEU cc_start: 0.9504 (mt) cc_final: 0.9244 (mm) REVERT: G 780 ASN cc_start: 0.8219 (p0) cc_final: 0.7838 (p0) REVERT: G 787 TYR cc_start: 0.8853 (m-10) cc_final: 0.8562 (m-80) REVERT: G 803 LYS cc_start: 0.8694 (mttt) cc_final: 0.8313 (mttm) REVERT: G 853 MET cc_start: 0.8079 (ppp) cc_final: 0.7762 (ppp) REVERT: G 856 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8911 (ttpp) REVERT: H 771 ASP cc_start: 0.8921 (t0) cc_final: 0.6949 (p0) REVERT: H 772 LEU cc_start: 0.9390 (mp) cc_final: 0.9059 (mp) REVERT: H 807 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6106 (tm-30) REVERT: H 824 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 825 MET cc_start: 0.8585 (pmm) cc_final: 0.8280 (pmm) REVERT: H 858 LEU cc_start: 0.7951 (tp) cc_final: 0.7694 (tp) REVERT: H 868 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7706 (mmm-85) REVERT: I 762 MET cc_start: 0.8260 (mtm) cc_final: 0.7963 (mtt) REVERT: I 807 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6221 (tm-30) REVERT: I 856 LYS cc_start: 0.8982 (tmmt) cc_final: 0.8479 (tttm) REVERT: I 870 LEU cc_start: 0.9355 (tp) cc_final: 0.8816 (tt) REVERT: J 762 MET cc_start: 0.7494 (mtt) cc_final: 0.6946 (mtt) REVERT: J 807 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6739 (tm-30) REVERT: J 868 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7897 (mmm-85) REVERT: J 870 LEU cc_start: 0.8965 (tp) cc_final: 0.8681 (tt) REVERT: K 762 MET cc_start: 0.8368 (mtm) cc_final: 0.7938 (mtt) REVERT: K 807 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6361 (tm-30) REVERT: L 771 ASP cc_start: 0.8951 (t0) cc_final: 0.6844 (p0) REVERT: L 772 LEU cc_start: 0.9464 (mp) cc_final: 0.9066 (mp) REVERT: L 786 MET cc_start: 0.8119 (tpp) cc_final: 0.7561 (mmm) REVERT: L 807 GLU cc_start: 0.7092 (mt-10) cc_final: 0.5661 (tm-30) REVERT: L 817 ASP cc_start: 0.8618 (t70) cc_final: 0.8338 (t0) REVERT: L 866 ASP cc_start: 0.8535 (m-30) cc_final: 0.8203 (m-30) REVERT: L 868 ARG cc_start: 0.8607 (mmt180) cc_final: 0.7809 (mmm-85) REVERT: M 762 MET cc_start: 0.8320 (mtm) cc_final: 0.7832 (mtt) REVERT: M 771 ASP cc_start: 0.9069 (t0) cc_final: 0.7507 (p0) REVERT: M 786 MET cc_start: 0.8866 (tpp) cc_final: 0.8554 (tpp) REVERT: M 807 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6030 (tm-30) REVERT: M 817 ASP cc_start: 0.8833 (t0) cc_final: 0.8609 (t0) REVERT: M 824 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8320 (tm-30) REVERT: M 858 LEU cc_start: 0.8223 (tp) cc_final: 0.7747 (tp) REVERT: N 762 MET cc_start: 0.7108 (mtt) cc_final: 0.6554 (mtt) REVERT: N 771 ASP cc_start: 0.8986 (t0) cc_final: 0.6998 (p0) REVERT: N 772 LEU cc_start: 0.9513 (mp) cc_final: 0.9212 (mp) REVERT: N 807 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6571 (tm-30) REVERT: N 824 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7899 (tm-30) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2420 time to fit residues: 138.0415 Evaluate side-chains 325 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13538 Z= 0.304 Angle : 0.758 8.513 18298 Z= 0.392 Chirality : 0.044 0.147 1918 Planarity : 0.006 0.066 2394 Dihedral : 6.545 23.317 1820 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.51 % Favored : 82.49 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.16), residues: 1582 helix: -2.98 (0.34), residues: 168 sheet: -1.75 (0.39), residues: 168 loop : -3.98 (0.13), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 765 PHE 0.014 0.002 PHE J 774 TYR 0.018 0.002 TYR G 800 ARG 0.008 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 MET cc_start: 0.6627 (mtt) cc_final: 0.6083 (mtt) REVERT: A 824 GLU cc_start: 0.8986 (tp30) cc_final: 0.7858 (tm-30) REVERT: A 870 LEU cc_start: 0.9649 (tp) cc_final: 0.9408 (tp) REVERT: B 780 ASN cc_start: 0.8344 (p0) cc_final: 0.8127 (p0) REVERT: B 787 TYR cc_start: 0.9091 (m-10) cc_final: 0.8766 (m-10) REVERT: B 800 TYR cc_start: 0.8718 (t80) cc_final: 0.8439 (t80) REVERT: B 803 LYS cc_start: 0.8854 (mttt) cc_final: 0.8562 (mttm) REVERT: B 807 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 824 GLU cc_start: 0.8865 (tp30) cc_final: 0.8036 (tm-30) REVERT: B 829 LEU cc_start: 0.9598 (mt) cc_final: 0.9127 (mt) REVERT: C 759 GLN cc_start: 0.9034 (pm20) cc_final: 0.8810 (pm20) REVERT: C 762 MET cc_start: 0.7469 (mtt) cc_final: 0.6673 (mtt) REVERT: C 786 MET cc_start: 0.8355 (tpp) cc_final: 0.7995 (tpp) REVERT: C 856 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8574 (ttpp) REVERT: C 866 ASP cc_start: 0.8625 (m-30) cc_final: 0.7571 (t0) REVERT: C 870 LEU cc_start: 0.9468 (tt) cc_final: 0.9137 (tt) REVERT: D 762 MET cc_start: 0.7117 (mtt) cc_final: 0.6659 (mtt) REVERT: D 780 ASN cc_start: 0.8841 (p0) cc_final: 0.8317 (p0) REVERT: D 787 TYR cc_start: 0.8873 (m-80) cc_final: 0.8536 (m-80) REVERT: D 791 THR cc_start: 0.8427 (p) cc_final: 0.8218 (p) REVERT: D 800 TYR cc_start: 0.8421 (t80) cc_final: 0.8167 (t80) REVERT: D 856 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8398 (ttpp) REVERT: E 762 MET cc_start: 0.7382 (mtt) cc_final: 0.6808 (mtt) REVERT: E 787 TYR cc_start: 0.8972 (m-10) cc_final: 0.8159 (m-10) REVERT: E 791 THR cc_start: 0.8629 (p) cc_final: 0.8380 (p) REVERT: E 800 TYR cc_start: 0.8717 (t80) cc_final: 0.8448 (t80) REVERT: E 825 MET cc_start: 0.8073 (tpp) cc_final: 0.7502 (mmm) REVERT: E 829 LEU cc_start: 0.9539 (mt) cc_final: 0.9283 (mt) REVERT: E 858 LEU cc_start: 0.8890 (tp) cc_final: 0.8685 (tp) REVERT: E 860 ILE cc_start: 0.8304 (mm) cc_final: 0.7700 (mp) REVERT: E 866 ASP cc_start: 0.8888 (m-30) cc_final: 0.8120 (t0) REVERT: E 868 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7752 (mmm-85) REVERT: F 762 MET cc_start: 0.7068 (mtt) cc_final: 0.6568 (mtt) REVERT: F 807 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8160 (mm-30) REVERT: F 816 LYS cc_start: 0.9050 (pptt) cc_final: 0.8820 (pptt) REVERT: F 824 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8009 (tm-30) REVERT: F 825 MET cc_start: 0.7944 (mtt) cc_final: 0.7330 (mtt) REVERT: F 850 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7457 (mp0) REVERT: G 759 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8653 (tm-30) REVERT: G 762 MET cc_start: 0.7228 (mtt) cc_final: 0.6278 (mtt) REVERT: G 772 LEU cc_start: 0.9528 (mt) cc_final: 0.9262 (mm) REVERT: G 780 ASN cc_start: 0.8279 (p0) cc_final: 0.8006 (p0) REVERT: G 787 TYR cc_start: 0.9025 (m-10) cc_final: 0.8287 (m-80) REVERT: G 791 THR cc_start: 0.8527 (p) cc_final: 0.8318 (p) REVERT: G 803 LYS cc_start: 0.8621 (mttt) cc_final: 0.8283 (mttm) REVERT: G 829 LEU cc_start: 0.9536 (mt) cc_final: 0.9192 (mt) REVERT: G 853 MET cc_start: 0.8402 (ppp) cc_final: 0.7543 (ppp) REVERT: G 856 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8894 (ttpp) REVERT: H 771 ASP cc_start: 0.8973 (t0) cc_final: 0.7172 (p0) REVERT: H 772 LEU cc_start: 0.9448 (mp) cc_final: 0.9063 (mp) REVERT: H 807 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6019 (tm-30) REVERT: H 824 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7867 (tm-30) REVERT: H 825 MET cc_start: 0.8581 (pmm) cc_final: 0.8367 (pmm) REVERT: H 868 ARG cc_start: 0.8272 (mmt180) cc_final: 0.7808 (mmm-85) REVERT: I 762 MET cc_start: 0.8372 (mtm) cc_final: 0.7894 (mtt) REVERT: I 775 ASN cc_start: 0.8502 (t0) cc_final: 0.8293 (t0) REVERT: I 807 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6190 (tm-30) REVERT: I 856 LYS cc_start: 0.8845 (tmmt) cc_final: 0.8434 (tttm) REVERT: I 866 ASP cc_start: 0.8726 (m-30) cc_final: 0.8162 (m-30) REVERT: I 870 LEU cc_start: 0.9265 (tp) cc_final: 0.8744 (tt) REVERT: J 762 MET cc_start: 0.7543 (mtt) cc_final: 0.7024 (mtt) REVERT: J 807 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6805 (tm-30) REVERT: J 868 ARG cc_start: 0.8364 (mmt180) cc_final: 0.7908 (mmm-85) REVERT: J 870 LEU cc_start: 0.8955 (tp) cc_final: 0.8727 (tt) REVERT: K 762 MET cc_start: 0.8325 (mtm) cc_final: 0.7855 (mtt) REVERT: K 807 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6419 (tm-30) REVERT: K 868 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7677 (mmm-85) REVERT: L 786 MET cc_start: 0.8098 (tpp) cc_final: 0.7689 (mmm) REVERT: L 807 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6233 (tm-30) REVERT: L 817 ASP cc_start: 0.8644 (t70) cc_final: 0.8417 (t0) REVERT: L 824 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7862 (tm-30) REVERT: L 868 ARG cc_start: 0.8527 (mmt180) cc_final: 0.7772 (mmm-85) REVERT: M 762 MET cc_start: 0.8391 (mtm) cc_final: 0.7834 (mtt) REVERT: M 771 ASP cc_start: 0.8995 (t0) cc_final: 0.7462 (p0) REVERT: M 786 MET cc_start: 0.8788 (tpp) cc_final: 0.8585 (tpp) REVERT: M 807 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6016 (tm-30) REVERT: M 817 ASP cc_start: 0.8845 (t0) cc_final: 0.8602 (t0) REVERT: M 824 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8535 (tm-30) REVERT: M 858 LEU cc_start: 0.8255 (tp) cc_final: 0.7794 (tp) REVERT: N 762 MET cc_start: 0.7160 (mtt) cc_final: 0.6590 (mtt) REVERT: N 786 MET cc_start: 0.8944 (tpp) cc_final: 0.8728 (tpp) REVERT: N 807 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6250 (tm-30) REVERT: N 824 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7908 (tm-30) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.2353 time to fit residues: 132.9677 Evaluate side-chains 322 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13538 Z= 0.373 Angle : 0.817 8.750 18298 Z= 0.424 Chirality : 0.045 0.199 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.756 21.959 1820 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.60 % Favored : 80.40 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.16), residues: 1582 helix: -2.97 (0.34), residues: 168 sheet: -1.77 (0.38), residues: 168 loop : -3.95 (0.13), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS G 765 PHE 0.019 0.002 PHE J 774 TYR 0.024 0.002 TYR B 861 ARG 0.008 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 MET cc_start: 0.6747 (mtt) cc_final: 0.6227 (mtt) REVERT: A 824 GLU cc_start: 0.8925 (tp30) cc_final: 0.7863 (tm-30) REVERT: A 825 MET cc_start: 0.8120 (mtt) cc_final: 0.7641 (mtp) REVERT: A 853 MET cc_start: 0.7997 (ppp) cc_final: 0.7746 (ppp) REVERT: A 860 ILE cc_start: 0.8330 (mp) cc_final: 0.6847 (mp) REVERT: A 870 LEU cc_start: 0.9641 (tp) cc_final: 0.9325 (tp) REVERT: B 780 ASN cc_start: 0.8379 (p0) cc_final: 0.8094 (p0) REVERT: B 787 TYR cc_start: 0.9084 (m-10) cc_final: 0.8668 (m-10) REVERT: B 800 TYR cc_start: 0.8732 (t80) cc_final: 0.8453 (t80) REVERT: B 803 LYS cc_start: 0.8790 (mttt) cc_final: 0.8514 (mttm) REVERT: B 807 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8277 (mm-30) REVERT: B 824 GLU cc_start: 0.8896 (tp30) cc_final: 0.8093 (tm-30) REVERT: B 829 LEU cc_start: 0.9603 (mt) cc_final: 0.9149 (mt) REVERT: C 762 MET cc_start: 0.7671 (mtt) cc_final: 0.7094 (mtt) REVERT: C 787 TYR cc_start: 0.8815 (m-10) cc_final: 0.8309 (m-10) REVERT: C 856 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8632 (ttpp) REVERT: C 866 ASP cc_start: 0.8509 (m-30) cc_final: 0.7699 (t0) REVERT: C 870 LEU cc_start: 0.9467 (tt) cc_final: 0.9203 (tt) REVERT: D 759 GLN cc_start: 0.8763 (pm20) cc_final: 0.8500 (pm20) REVERT: D 762 MET cc_start: 0.7227 (mtt) cc_final: 0.6802 (mtt) REVERT: D 780 ASN cc_start: 0.8933 (p0) cc_final: 0.8330 (p0) REVERT: D 787 TYR cc_start: 0.9031 (m-80) cc_final: 0.8626 (m-80) REVERT: D 791 THR cc_start: 0.8476 (p) cc_final: 0.8276 (p) REVERT: D 800 TYR cc_start: 0.8376 (t80) cc_final: 0.8143 (t80) REVERT: E 762 MET cc_start: 0.7402 (mtt) cc_final: 0.6906 (mtt) REVERT: E 787 TYR cc_start: 0.8895 (m-10) cc_final: 0.7833 (m-80) REVERT: E 791 THR cc_start: 0.8724 (p) cc_final: 0.8478 (p) REVERT: E 800 TYR cc_start: 0.8690 (t80) cc_final: 0.8420 (t80) REVERT: E 825 MET cc_start: 0.8163 (tpp) cc_final: 0.7931 (tpt) REVERT: E 829 LEU cc_start: 0.9496 (mt) cc_final: 0.9194 (mt) REVERT: E 860 ILE cc_start: 0.8028 (mm) cc_final: 0.6670 (mp) REVERT: E 866 ASP cc_start: 0.8894 (m-30) cc_final: 0.8145 (t0) REVERT: E 868 ARG cc_start: 0.7780 (mmt90) cc_final: 0.7567 (mmm-85) REVERT: E 869 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7530 (mt-10) REVERT: F 759 GLN cc_start: 0.8844 (pm20) cc_final: 0.8551 (pm20) REVERT: F 762 MET cc_start: 0.7124 (mtt) cc_final: 0.6663 (mtt) REVERT: F 807 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8180 (mm-30) REVERT: F 816 LYS cc_start: 0.9054 (pptt) cc_final: 0.8787 (ptmt) REVERT: F 824 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8056 (tm-30) REVERT: F 825 MET cc_start: 0.8193 (mtt) cc_final: 0.7935 (mtp) REVERT: G 759 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8643 (tm-30) REVERT: G 762 MET cc_start: 0.7268 (mtt) cc_final: 0.6566 (mtt) REVERT: G 772 LEU cc_start: 0.9527 (mt) cc_final: 0.9281 (mm) REVERT: G 780 ASN cc_start: 0.8316 (p0) cc_final: 0.8064 (p0) REVERT: G 787 TYR cc_start: 0.9207 (m-10) cc_final: 0.8801 (m-10) REVERT: G 791 THR cc_start: 0.8571 (p) cc_final: 0.8349 (p) REVERT: G 803 LYS cc_start: 0.8716 (mttt) cc_final: 0.8388 (mttm) REVERT: G 829 LEU cc_start: 0.9562 (mt) cc_final: 0.9349 (mt) REVERT: G 853 MET cc_start: 0.8211 (ppp) cc_final: 0.7549 (ppp) REVERT: G 860 ILE cc_start: 0.8770 (mp) cc_final: 0.7291 (mp) REVERT: H 771 ASP cc_start: 0.9033 (t0) cc_final: 0.7208 (p0) REVERT: H 772 LEU cc_start: 0.9488 (mp) cc_final: 0.9039 (mp) REVERT: H 807 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6032 (tm-30) REVERT: H 824 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7914 (tm-30) REVERT: H 825 MET cc_start: 0.8597 (pmm) cc_final: 0.8378 (pmm) REVERT: H 856 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8606 (ttpp) REVERT: H 868 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7862 (mmm-85) REVERT: I 762 MET cc_start: 0.8517 (mtm) cc_final: 0.8217 (mtt) REVERT: I 775 ASN cc_start: 0.8561 (t0) cc_final: 0.8301 (t0) REVERT: I 787 TYR cc_start: 0.8063 (m-80) cc_final: 0.7679 (m-80) REVERT: I 807 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6287 (tm-30) REVERT: I 856 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8084 (tttm) REVERT: I 869 GLU cc_start: 0.8062 (mp0) cc_final: 0.7557 (mp0) REVERT: I 870 LEU cc_start: 0.9100 (tp) cc_final: 0.8709 (tt) REVERT: J 762 MET cc_start: 0.7595 (mtt) cc_final: 0.6976 (mtt) REVERT: J 807 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6693 (tm-30) REVERT: J 868 ARG cc_start: 0.8427 (mmt180) cc_final: 0.7972 (mmm-85) REVERT: J 870 LEU cc_start: 0.9003 (tp) cc_final: 0.8786 (tt) REVERT: K 762 MET cc_start: 0.8407 (mtm) cc_final: 0.7898 (mtt) REVERT: K 807 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6241 (tm-30) REVERT: L 786 MET cc_start: 0.7938 (tpp) cc_final: 0.7426 (mmm) REVERT: L 807 GLU cc_start: 0.7820 (mt-10) cc_final: 0.6727 (tm-30) REVERT: L 817 ASP cc_start: 0.8680 (t70) cc_final: 0.8456 (t0) REVERT: L 824 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8026 (tm-30) REVERT: L 868 ARG cc_start: 0.8638 (mmt180) cc_final: 0.8337 (mmm-85) REVERT: M 762 MET cc_start: 0.8290 (mtm) cc_final: 0.7838 (mtt) REVERT: M 786 MET cc_start: 0.8673 (tpp) cc_final: 0.8453 (tpp) REVERT: M 807 GLU cc_start: 0.7179 (mt-10) cc_final: 0.5873 (tm-30) REVERT: M 817 ASP cc_start: 0.8872 (t0) cc_final: 0.8647 (t0) REVERT: M 824 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8443 (tm-30) REVERT: M 858 LEU cc_start: 0.8248 (tp) cc_final: 0.7817 (tp) REVERT: N 762 MET cc_start: 0.7294 (mtt) cc_final: 0.6662 (mtt) REVERT: N 771 ASP cc_start: 0.8902 (t70) cc_final: 0.6868 (p0) REVERT: N 807 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6213 (tm-30) REVERT: N 824 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7971 (tm-30) REVERT: N 858 LEU cc_start: 0.8160 (tp) cc_final: 0.7854 (mt) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.2412 time to fit residues: 135.5009 Evaluate side-chains 323 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 802 GLN N 765 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13538 Z= 0.319 Angle : 0.795 9.242 18298 Z= 0.411 Chirality : 0.045 0.194 1918 Planarity : 0.007 0.067 2394 Dihedral : 6.635 23.089 1820 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.17), residues: 1582 helix: -3.11 (0.32), residues: 182 sheet: -1.84 (0.39), residues: 168 loop : -3.86 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS F 765 PHE 0.018 0.002 PHE F 788 TYR 0.019 0.002 TYR G 800 ARG 0.007 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.8908 (pm20) cc_final: 0.8694 (pm20) REVERT: A 762 MET cc_start: 0.7025 (mtt) cc_final: 0.6348 (mtt) REVERT: A 800 TYR cc_start: 0.8410 (t80) cc_final: 0.8103 (t80) REVERT: A 824 GLU cc_start: 0.8972 (tp30) cc_final: 0.7925 (tm-30) REVERT: A 825 MET cc_start: 0.8090 (mtt) cc_final: 0.7434 (mtt) REVERT: A 853 MET cc_start: 0.8215 (ppp) cc_final: 0.7959 (ppp) REVERT: A 860 ILE cc_start: 0.7957 (mp) cc_final: 0.7742 (mp) REVERT: A 870 LEU cc_start: 0.9598 (tp) cc_final: 0.9263 (tp) REVERT: B 759 GLN cc_start: 0.9030 (pm20) cc_final: 0.8682 (pm20) REVERT: B 762 MET cc_start: 0.8164 (mpp) cc_final: 0.7706 (mpp) REVERT: B 787 TYR cc_start: 0.9004 (m-10) cc_final: 0.8676 (m-10) REVERT: B 803 LYS cc_start: 0.8772 (mttt) cc_final: 0.8463 (mttm) REVERT: B 824 GLU cc_start: 0.8886 (tp30) cc_final: 0.8116 (tm-30) REVERT: B 829 LEU cc_start: 0.9593 (mt) cc_final: 0.9133 (mt) REVERT: B 868 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7924 (mmt90) REVERT: C 759 GLN cc_start: 0.9055 (pm20) cc_final: 0.8808 (pm20) REVERT: C 762 MET cc_start: 0.7593 (mtt) cc_final: 0.7024 (mtt) REVERT: C 825 MET cc_start: 0.8590 (tpt) cc_final: 0.7669 (tpt) REVERT: C 866 ASP cc_start: 0.8653 (m-30) cc_final: 0.7589 (t0) REVERT: D 759 GLN cc_start: 0.8822 (pm20) cc_final: 0.8493 (pm20) REVERT: D 762 MET cc_start: 0.7163 (mtt) cc_final: 0.6720 (mtt) REVERT: D 780 ASN cc_start: 0.8901 (p0) cc_final: 0.8320 (p0) REVERT: D 787 TYR cc_start: 0.9126 (m-80) cc_final: 0.8597 (m-80) REVERT: D 791 THR cc_start: 0.8443 (p) cc_final: 0.8218 (p) REVERT: D 856 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8461 (ttpp) REVERT: E 762 MET cc_start: 0.7359 (mtt) cc_final: 0.6866 (mtt) REVERT: E 787 TYR cc_start: 0.8943 (m-10) cc_final: 0.8403 (m-10) REVERT: E 791 THR cc_start: 0.8699 (p) cc_final: 0.8458 (p) REVERT: E 800 TYR cc_start: 0.8633 (t80) cc_final: 0.8392 (t80) REVERT: E 825 MET cc_start: 0.8206 (tpp) cc_final: 0.7909 (tpt) REVERT: E 829 LEU cc_start: 0.9521 (mt) cc_final: 0.9261 (mt) REVERT: E 860 ILE cc_start: 0.8168 (mm) cc_final: 0.6707 (mp) REVERT: E 866 ASP cc_start: 0.8887 (m-30) cc_final: 0.8202 (t0) REVERT: E 868 ARG cc_start: 0.7783 (mmt90) cc_final: 0.7573 (mmm-85) REVERT: E 869 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7250 (mt-10) REVERT: E 870 LEU cc_start: 0.9624 (tp) cc_final: 0.9258 (tt) REVERT: F 759 GLN cc_start: 0.8931 (pm20) cc_final: 0.8671 (pm20) REVERT: F 762 MET cc_start: 0.7029 (mtt) cc_final: 0.6563 (mtt) REVERT: F 807 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8120 (mm-30) REVERT: F 816 LYS cc_start: 0.9030 (pptt) cc_final: 0.8786 (pptt) REVERT: F 824 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7955 (tm-30) REVERT: F 850 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7433 (mt-10) REVERT: G 759 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8655 (tm-30) REVERT: G 762 MET cc_start: 0.7176 (mtt) cc_final: 0.6433 (mtt) REVERT: G 772 LEU cc_start: 0.9497 (mt) cc_final: 0.9261 (mm) REVERT: G 780 ASN cc_start: 0.8336 (p0) cc_final: 0.8110 (p0) REVERT: G 787 TYR cc_start: 0.8909 (m-10) cc_final: 0.8403 (m-80) REVERT: G 791 THR cc_start: 0.8615 (p) cc_final: 0.8392 (p) REVERT: G 803 LYS cc_start: 0.8669 (mttt) cc_final: 0.8308 (mttm) REVERT: G 829 LEU cc_start: 0.9548 (mt) cc_final: 0.9189 (mt) REVERT: G 853 MET cc_start: 0.8349 (ppp) cc_final: 0.8068 (ppp) REVERT: G 860 ILE cc_start: 0.8586 (mp) cc_final: 0.7730 (mp) REVERT: G 869 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7183 (mt-10) REVERT: H 771 ASP cc_start: 0.9018 (t0) cc_final: 0.7229 (p0) REVERT: H 772 LEU cc_start: 0.9505 (mp) cc_final: 0.9019 (mp) REVERT: H 807 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6034 (tm-30) REVERT: H 824 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7908 (tm-30) REVERT: H 825 MET cc_start: 0.8497 (pmm) cc_final: 0.8223 (pmm) REVERT: H 856 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8587 (ttpp) REVERT: H 868 ARG cc_start: 0.8201 (mmt180) cc_final: 0.7840 (mmm-85) REVERT: I 762 MET cc_start: 0.8567 (mtm) cc_final: 0.8218 (mtt) REVERT: I 775 ASN cc_start: 0.8524 (t0) cc_final: 0.8297 (t0) REVERT: I 787 TYR cc_start: 0.8081 (m-80) cc_final: 0.7695 (m-80) REVERT: I 807 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6306 (tm-30) REVERT: I 856 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8335 (tttp) REVERT: I 869 GLU cc_start: 0.8191 (mp0) cc_final: 0.7848 (mp0) REVERT: J 762 MET cc_start: 0.7588 (mtt) cc_final: 0.6911 (mtt) REVERT: J 807 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6643 (tm-30) REVERT: J 868 ARG cc_start: 0.8469 (mmt180) cc_final: 0.8121 (mmm-85) REVERT: J 870 LEU cc_start: 0.9000 (tp) cc_final: 0.8792 (tt) REVERT: K 762 MET cc_start: 0.8494 (mtm) cc_final: 0.8011 (mtt) REVERT: K 786 MET cc_start: 0.8729 (tpp) cc_final: 0.8453 (mmm) REVERT: K 807 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6166 (tm-30) REVERT: L 786 MET cc_start: 0.8107 (tpp) cc_final: 0.7545 (mmm) REVERT: L 807 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6616 (tm-30) REVERT: L 824 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7987 (tm-30) REVERT: L 868 ARG cc_start: 0.8639 (mmt180) cc_final: 0.8332 (mmm-85) REVERT: M 762 MET cc_start: 0.8539 (mtm) cc_final: 0.7878 (mtt) REVERT: M 786 MET cc_start: 0.8759 (tpp) cc_final: 0.8530 (tpp) REVERT: M 807 GLU cc_start: 0.7140 (mt-10) cc_final: 0.5984 (tm-30) REVERT: M 817 ASP cc_start: 0.8886 (t0) cc_final: 0.8680 (t0) REVERT: M 824 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8333 (tm-30) REVERT: M 858 LEU cc_start: 0.8173 (tp) cc_final: 0.7804 (tp) REVERT: N 762 MET cc_start: 0.7185 (mtt) cc_final: 0.6559 (mtt) REVERT: N 771 ASP cc_start: 0.8907 (t70) cc_final: 0.7162 (p0) REVERT: N 786 MET cc_start: 0.9005 (tpp) cc_final: 0.8775 (tpp) REVERT: N 807 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6181 (tm-30) REVERT: N 824 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7543 (tm-30) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.2388 time to fit residues: 133.7133 Evaluate side-chains 333 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13538 Z= 0.190 Angle : 0.720 8.715 18298 Z= 0.370 Chirality : 0.044 0.200 1918 Planarity : 0.006 0.066 2394 Dihedral : 6.123 22.639 1820 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.66 % Favored : 85.34 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -4.98 (0.17), residues: 1582 helix: -2.79 (0.36), residues: 168 sheet: -3.12 (0.26), residues: 308 loop : -3.72 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 765 PHE 0.011 0.001 PHE H 788 TYR 0.021 0.001 TYR B 861 ARG 0.014 0.001 ARG J 805 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.8952 (pm20) cc_final: 0.8676 (pm20) REVERT: A 762 MET cc_start: 0.6696 (mtt) cc_final: 0.6061 (mtt) REVERT: A 800 TYR cc_start: 0.8413 (t80) cc_final: 0.8114 (t80) REVERT: A 824 GLU cc_start: 0.8902 (tp30) cc_final: 0.7952 (tm-30) REVERT: A 825 MET cc_start: 0.7861 (mtt) cc_final: 0.7149 (mtt) REVERT: A 853 MET cc_start: 0.8358 (ppp) cc_final: 0.8079 (ppp) REVERT: A 870 LEU cc_start: 0.9577 (tp) cc_final: 0.9363 (tp) REVERT: B 762 MET cc_start: 0.7959 (mpp) cc_final: 0.7504 (mpp) REVERT: B 803 LYS cc_start: 0.8569 (mttt) cc_final: 0.8226 (mmtp) REVERT: B 824 GLU cc_start: 0.8848 (tp30) cc_final: 0.8068 (tm-30) REVERT: B 829 LEU cc_start: 0.9563 (mt) cc_final: 0.9052 (mt) REVERT: B 866 ASP cc_start: 0.8821 (m-30) cc_final: 0.8418 (t0) REVERT: B 868 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7606 (mmm-85) REVERT: C 759 GLN cc_start: 0.9027 (pm20) cc_final: 0.8769 (pm20) REVERT: C 762 MET cc_start: 0.7370 (mtt) cc_final: 0.6893 (mtt) REVERT: C 825 MET cc_start: 0.8459 (tpt) cc_final: 0.7669 (tpt) REVERT: C 829 LEU cc_start: 0.9601 (mt) cc_final: 0.9059 (mt) REVERT: C 860 ILE cc_start: 0.8652 (mp) cc_final: 0.8221 (mp) REVERT: C 866 ASP cc_start: 0.8554 (m-30) cc_final: 0.7559 (t0) REVERT: D 759 GLN cc_start: 0.8883 (pm20) cc_final: 0.8450 (pm20) REVERT: D 762 MET cc_start: 0.7396 (mtt) cc_final: 0.6538 (mtt) REVERT: D 780 ASN cc_start: 0.8724 (p0) cc_final: 0.8241 (p0) REVERT: D 787 TYR cc_start: 0.9065 (m-80) cc_final: 0.8393 (m-80) REVERT: D 791 THR cc_start: 0.8207 (p) cc_final: 0.7950 (p) REVERT: D 856 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8482 (ttpp) REVERT: E 762 MET cc_start: 0.7253 (mtt) cc_final: 0.6716 (mtt) REVERT: E 787 TYR cc_start: 0.8719 (m-10) cc_final: 0.8102 (m-80) REVERT: E 791 THR cc_start: 0.8539 (p) cc_final: 0.8276 (p) REVERT: E 799 ASP cc_start: 0.7983 (p0) cc_final: 0.7629 (p0) REVERT: E 807 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 825 MET cc_start: 0.6916 (mmt) cc_final: 0.6429 (mmt) REVERT: E 829 LEU cc_start: 0.9504 (mt) cc_final: 0.9288 (mt) REVERT: E 860 ILE cc_start: 0.8065 (mm) cc_final: 0.6643 (mp) REVERT: E 866 ASP cc_start: 0.8691 (m-30) cc_final: 0.8119 (t0) REVERT: E 868 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7666 (mmm-85) REVERT: E 869 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7543 (mt-10) REVERT: E 870 LEU cc_start: 0.9554 (tp) cc_final: 0.9204 (tt) REVERT: F 762 MET cc_start: 0.6659 (mtt) cc_final: 0.6270 (mtt) REVERT: F 807 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7907 (mm-30) REVERT: F 824 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7829 (tm-30) REVERT: F 850 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7216 (mt-10) REVERT: F 868 ARG cc_start: 0.7777 (mmt90) cc_final: 0.7132 (mmm-85) REVERT: G 762 MET cc_start: 0.6961 (mtt) cc_final: 0.6277 (mtt) REVERT: G 772 LEU cc_start: 0.9420 (mt) cc_final: 0.9155 (mm) REVERT: G 780 ASN cc_start: 0.8318 (p0) cc_final: 0.7996 (p0) REVERT: G 787 TYR cc_start: 0.8809 (m-10) cc_final: 0.8427 (m-80) REVERT: G 791 THR cc_start: 0.8348 (p) cc_final: 0.8111 (p) REVERT: G 803 LYS cc_start: 0.8520 (mttt) cc_final: 0.8165 (mmtp) REVERT: G 829 LEU cc_start: 0.9548 (mt) cc_final: 0.9334 (mt) REVERT: G 858 LEU cc_start: 0.8837 (tp) cc_final: 0.8447 (tp) REVERT: H 771 ASP cc_start: 0.8963 (t0) cc_final: 0.7191 (p0) REVERT: H 772 LEU cc_start: 0.9488 (mp) cc_final: 0.8966 (mp) REVERT: H 824 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 856 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8429 (tmtt) REVERT: H 868 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7638 (mmm-85) REVERT: I 762 MET cc_start: 0.8581 (mtm) cc_final: 0.8150 (mtt) REVERT: I 807 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6131 (tm-30) REVERT: I 869 GLU cc_start: 0.8131 (mp0) cc_final: 0.7835 (mp0) REVERT: J 762 MET cc_start: 0.7336 (mtt) cc_final: 0.6796 (mtt) REVERT: J 807 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6478 (tm-30) REVERT: J 868 ARG cc_start: 0.8213 (mmt180) cc_final: 0.7703 (mmm-85) REVERT: K 762 MET cc_start: 0.8432 (mtm) cc_final: 0.7950 (mtt) REVERT: K 807 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6248 (tm-30) REVERT: K 842 LEU cc_start: 0.9359 (mm) cc_final: 0.9143 (mm) REVERT: K 868 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8000 (mmm160) REVERT: L 786 MET cc_start: 0.8194 (tpp) cc_final: 0.7784 (mmm) REVERT: L 807 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6533 (tm-30) REVERT: L 817 ASP cc_start: 0.8707 (t70) cc_final: 0.8436 (t0) REVERT: L 824 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7969 (tm-30) REVERT: L 868 ARG cc_start: 0.8758 (mmt180) cc_final: 0.8521 (mmm-85) REVERT: M 762 MET cc_start: 0.8621 (mtm) cc_final: 0.8050 (mtt) REVERT: M 786 MET cc_start: 0.8882 (tpp) cc_final: 0.8593 (tpp) REVERT: M 807 GLU cc_start: 0.6923 (mt-10) cc_final: 0.5742 (tm-30) REVERT: M 817 ASP cc_start: 0.8867 (t0) cc_final: 0.8651 (t0) REVERT: M 824 GLU cc_start: 0.8682 (tm-30) cc_final: 0.7888 (tm-30) REVERT: M 859 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7375 (mtm-85) REVERT: M 866 ASP cc_start: 0.9032 (m-30) cc_final: 0.8729 (t70) REVERT: N 762 MET cc_start: 0.7053 (mtt) cc_final: 0.6387 (mtt) REVERT: N 807 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6410 (tm-30) REVERT: N 817 ASP cc_start: 0.9042 (t70) cc_final: 0.8822 (t0) REVERT: N 824 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7533 (tm-30) REVERT: N 855 TYR cc_start: 0.6756 (m-10) cc_final: 0.6501 (m-80) REVERT: N 856 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8770 (ptmm) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2447 time to fit residues: 144.7829 Evaluate side-chains 350 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 851 ASN ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 759 GLN ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13538 Z= 0.384 Angle : 0.858 8.373 18298 Z= 0.443 Chirality : 0.046 0.158 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.596 22.733 1820 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.86 % Favored : 79.14 % Rotamer: Outliers : 0.07 % Allowed : 0.42 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.17), residues: 1582 helix: -2.99 (0.33), residues: 182 sheet: -1.90 (0.39), residues: 168 loop : -3.80 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 765 PHE 0.021 0.002 PHE J 774 TYR 0.030 0.002 TYR E 861 ARG 0.010 0.001 ARG J 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.8944 (pm20) cc_final: 0.8727 (pm20) REVERT: A 762 MET cc_start: 0.7024 (mtt) cc_final: 0.6325 (mtt) REVERT: A 800 TYR cc_start: 0.8401 (t80) cc_final: 0.8188 (t80) REVERT: A 824 GLU cc_start: 0.8895 (tp30) cc_final: 0.7839 (tm-30) REVERT: A 825 MET cc_start: 0.8161 (mtt) cc_final: 0.7513 (mtt) REVERT: A 853 MET cc_start: 0.7942 (ppp) cc_final: 0.7733 (ppp) REVERT: B 759 GLN cc_start: 0.8934 (pm20) cc_final: 0.8728 (pm20) REVERT: B 762 MET cc_start: 0.7990 (mpp) cc_final: 0.7493 (mpp) REVERT: B 791 THR cc_start: 0.8747 (p) cc_final: 0.8537 (p) REVERT: B 803 LYS cc_start: 0.8605 (mttt) cc_final: 0.8263 (mmtp) REVERT: B 824 GLU cc_start: 0.8886 (tp30) cc_final: 0.8128 (tm-30) REVERT: B 829 LEU cc_start: 0.9598 (mt) cc_final: 0.9062 (mt) REVERT: B 866 ASP cc_start: 0.8836 (m-30) cc_final: 0.8336 (t0) REVERT: B 868 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7807 (mmm-85) REVERT: C 759 GLN cc_start: 0.9105 (pm20) cc_final: 0.8828 (pm20) REVERT: C 762 MET cc_start: 0.7699 (mtt) cc_final: 0.7126 (mtt) REVERT: C 825 MET cc_start: 0.8495 (tpt) cc_final: 0.7624 (tpt) REVERT: C 851 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.6711 (t0) REVERT: C 860 ILE cc_start: 0.8406 (mp) cc_final: 0.6760 (mp) REVERT: C 866 ASP cc_start: 0.8651 (m-30) cc_final: 0.7570 (t0) REVERT: C 869 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7422 (mt-10) REVERT: D 759 GLN cc_start: 0.8948 (pm20) cc_final: 0.8548 (pm20) REVERT: D 762 MET cc_start: 0.7139 (mtt) cc_final: 0.6843 (mtt) REVERT: D 780 ASN cc_start: 0.8957 (p0) cc_final: 0.8377 (p0) REVERT: D 787 TYR cc_start: 0.9190 (m-80) cc_final: 0.8743 (m-80) REVERT: D 791 THR cc_start: 0.8447 (p) cc_final: 0.8215 (p) REVERT: E 762 MET cc_start: 0.7782 (mtt) cc_final: 0.7144 (mtt) REVERT: E 791 THR cc_start: 0.8717 (p) cc_final: 0.8489 (p) REVERT: E 799 ASP cc_start: 0.8415 (p0) cc_final: 0.8054 (p0) REVERT: E 824 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7466 (tm-30) REVERT: E 829 LEU cc_start: 0.9507 (mt) cc_final: 0.9240 (mt) REVERT: E 860 ILE cc_start: 0.7939 (mm) cc_final: 0.6564 (mp) REVERT: E 866 ASP cc_start: 0.8861 (m-30) cc_final: 0.8088 (t0) REVERT: E 868 ARG cc_start: 0.7850 (mmt90) cc_final: 0.7620 (mmm-85) REVERT: E 869 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7343 (mt-10) REVERT: F 762 MET cc_start: 0.7102 (mtt) cc_final: 0.6629 (mtt) REVERT: F 807 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8085 (mm-30) REVERT: F 824 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8002 (tm-30) REVERT: G 759 GLN cc_start: 0.9217 (pm20) cc_final: 0.8949 (pm20) REVERT: G 762 MET cc_start: 0.7468 (mtt) cc_final: 0.6724 (mtt) REVERT: G 772 LEU cc_start: 0.9513 (mt) cc_final: 0.9263 (mm) REVERT: G 803 LYS cc_start: 0.8628 (mttt) cc_final: 0.8241 (mttm) REVERT: G 825 MET cc_start: 0.8446 (tpp) cc_final: 0.8108 (tpp) REVERT: G 829 LEU cc_start: 0.9547 (mt) cc_final: 0.9235 (mt) REVERT: G 858 LEU cc_start: 0.8821 (tp) cc_final: 0.8425 (tp) REVERT: G 860 ILE cc_start: 0.8800 (mp) cc_final: 0.8121 (mp) REVERT: H 771 ASP cc_start: 0.9072 (t0) cc_final: 0.7322 (p0) REVERT: H 772 LEU cc_start: 0.9559 (mp) cc_final: 0.8943 (mp) REVERT: H 807 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6092 (tm-30) REVERT: H 824 GLU cc_start: 0.8649 (tm-30) cc_final: 0.7832 (tm-30) REVERT: H 856 LYS cc_start: 0.8904 (ttpp) cc_final: 0.8349 (tmtt) REVERT: H 868 ARG cc_start: 0.8248 (mmt180) cc_final: 0.7780 (mmm-85) REVERT: I 762 MET cc_start: 0.8603 (mtm) cc_final: 0.8136 (mtt) REVERT: I 775 ASN cc_start: 0.8483 (t0) cc_final: 0.8214 (t0) REVERT: I 807 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6294 (tm-30) REVERT: I 869 GLU cc_start: 0.8205 (mp0) cc_final: 0.7859 (mp0) REVERT: J 762 MET cc_start: 0.7629 (mtt) cc_final: 0.6919 (mtt) REVERT: J 783 ILE cc_start: 0.9490 (tt) cc_final: 0.9129 (mp) REVERT: J 807 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6540 (tm-30) REVERT: J 868 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7857 (mmm-85) REVERT: K 762 MET cc_start: 0.8439 (mtm) cc_final: 0.7967 (mtt) REVERT: L 786 MET cc_start: 0.7992 (tpp) cc_final: 0.7570 (mmm) REVERT: L 807 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6622 (tm-30) REVERT: L 824 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7511 (tm-30) REVERT: L 868 ARG cc_start: 0.8586 (mmt180) cc_final: 0.8275 (mmm-85) REVERT: M 762 MET cc_start: 0.8649 (mtm) cc_final: 0.7871 (mtt) REVERT: M 786 MET cc_start: 0.8726 (tpp) cc_final: 0.8500 (tpp) REVERT: M 807 GLU cc_start: 0.7179 (mt-10) cc_final: 0.5884 (tm-30) REVERT: M 817 ASP cc_start: 0.8863 (t0) cc_final: 0.8651 (t0) REVERT: M 824 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8332 (tm-30) REVERT: N 762 MET cc_start: 0.7517 (mtt) cc_final: 0.6808 (mtt) REVERT: N 807 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6384 (tm-30) REVERT: N 824 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7557 (tm-30) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2331 time to fit residues: 126.2564 Evaluate side-chains 315 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069785 restraints weight = 51835.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071453 restraints weight = 28755.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072580 restraints weight = 17967.496| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13538 Z= 0.195 Angle : 0.745 10.549 18298 Z= 0.380 Chirality : 0.044 0.182 1918 Planarity : 0.006 0.064 2394 Dihedral : 6.141 23.959 1820 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.18), residues: 1582 helix: -2.73 (0.36), residues: 168 sheet: -3.11 (0.26), residues: 308 loop : -3.65 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 765 PHE 0.012 0.001 PHE B 788 TYR 0.028 0.001 TYR D 861 ARG 0.009 0.001 ARG B 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.69 seconds wall clock time: 55 minutes 5.84 seconds (3305.84 seconds total)