Starting phenix.real_space_refine on Sun Dec 10 03:21:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2023/6oks_20103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2023/6oks_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_20103/12_2023/6oks_20103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2023/6oks_20103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2023/6oks_20103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2023/6oks_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-1.21rc1-5172/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: 7.24, per 1000 atoms: 0.55 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: 5.05 Conformation dependent library (CDL) restraints added in 2.5 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: 1.50 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: 3.13 Time building geometry restraints manager: 5.49 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 36.230 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.510 ------------------------------------------------------------------------------- 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 : 1.721 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 outliers start: 140 outliers final: 25 residues processed: 589 average time/residue: 0.2511 time to fit residues: 210.1174 Evaluate side-chains 313 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 288 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1118 time to fit residues: 7.4396 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.0050 chunk 89 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 overall best weight: 0.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 851 ASN I 792 GLN ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 792 GLN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13538 Z= 0.189 Angle : 0.684 6.512 18298 Z= 0.352 Chirality : 0.042 0.176 1918 Planarity : 0.006 0.068 2394 Dihedral : 6.505 23.727 1820 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % 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: -5.27 (0.14), residues: 1582 helix: -3.43 (0.32), residues: 84 sheet: -2.17 (0.38), residues: 168 loop : -4.12 (0.11), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 765 PHE 0.011 0.001 PHE I 788 TYR 0.017 0.001 TYR M 855 ARG 0.011 0.001 ARG G 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 442 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 440 time to evaluate : 1.608 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 442 average time/residue: 0.2505 time to fit residues: 158.2094 Evaluate side-chains 315 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0605 ------------------------------------------------------------------------------- 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: 8.9990 chunk 116 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 792 GLN ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 792 GLN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 792 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13538 Z= 0.230 Angle : 0.690 6.766 18298 Z= 0.360 Chirality : 0.042 0.149 1918 Planarity : 0.006 0.070 2394 Dihedral : 6.207 21.588 1820 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 0.21 % Allowed : 3.43 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.15), residues: 1582 helix: -4.05 (0.24), residues: 168 sheet: -1.84 (0.39), residues: 168 loop : -4.13 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 765 PHE 0.009 0.001 PHE B 774 TYR 0.015 0.001 TYR H 855 ARG 0.017 0.001 ARG K 868 *********************** 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 395 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 392 time to evaluate : 1.515 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 outliers start: 3 outliers final: 0 residues processed: 395 average time/residue: 0.2457 time to fit residues: 139.4470 Evaluate side-chains 302 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1208 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 851 ASN ** G 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 759 GLN ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13538 Z= 0.367 Angle : 0.820 7.909 18298 Z= 0.428 Chirality : 0.045 0.153 1918 Planarity : 0.007 0.078 2394 Dihedral : 6.881 23.158 1820 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.46 % Favored : 81.54 % Rotamer: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.16), residues: 1582 helix: -4.01 (0.23), residues: 182 sheet: -3.17 (0.26), residues: 308 loop : -4.09 (0.14), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS A 765 PHE 0.016 0.002 PHE G 774 TYR 0.024 0.002 TYR M 855 ARG 0.008 0.001 ARG I 859 *********************** 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 377 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 1.656 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 outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2436 time to fit residues: 132.1000 Evaluate side-chains 278 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0951 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 838 ASN ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 802 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** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 13538 Z= 0.535 Angle : 0.967 9.793 18298 Z= 0.502 Chirality : 0.049 0.192 1918 Planarity : 0.008 0.075 2394 Dihedral : 7.515 23.520 1820 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.68 % Favored : 78.32 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -5.21 (0.16), residues: 1582 helix: -3.57 (0.28), residues: 182 sheet: -1.68 (0.39), residues: 168 loop : -4.10 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS G 765 PHE 0.026 0.003 PHE J 774 TYR 0.024 0.002 TYR L 855 ARG 0.013 0.001 ARG L 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 355 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.736 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 outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2388 time to fit residues: 122.6925 Evaluate side-chains 273 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0117 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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** ** J 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** M 802 GLN ** 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: 0.8115 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13538 Z= 0.264 Angle : 0.774 9.295 18298 Z= 0.401 Chirality : 0.045 0.214 1918 Planarity : 0.007 0.065 2394 Dihedral : 6.795 23.299 1820 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.70 % Favored : 82.30 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -5.23 (0.16), residues: 1582 helix: -2.80 (0.36), residues: 154 sheet: -3.06 (0.27), residues: 308 loop : -4.01 (0.14), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 765 PHE 0.016 0.002 PHE C 788 TYR 0.020 0.001 TYR A 861 ARG 0.007 0.001 ARG K 859 *********************** 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 379 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.663 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 outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.2457 time to fit residues: 133.9965 Evaluate side-chains 293 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0792 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13538 Z= 0.191 Angle : 0.728 9.485 18298 Z= 0.373 Chirality : 0.044 0.194 1918 Planarity : 0.006 0.072 2394 Dihedral : 6.266 22.419 1820 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -5.12 (0.17), residues: 1582 helix: -2.96 (0.35), residues: 168 sheet: -3.05 (0.26), residues: 308 loop : -3.86 (0.14), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 765 PHE 0.019 0.001 PHE A 788 TYR 0.020 0.001 TYR D 861 ARG 0.008 0.001 ARG B 859 *********************** 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 383 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.497 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 outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2358 time to fit residues: 130.7492 Evaluate side-chains 306 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0952 ------------------------------------------------------------------------------- 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: 0.0000 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 0.0060 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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** ** J 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13538 Z= 0.252 Angle : 0.757 8.243 18298 Z= 0.390 Chirality : 0.044 0.182 1918 Planarity : 0.006 0.066 2394 Dihedral : 6.285 22.825 1820 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.57 % Favored : 82.43 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -4.77 (0.17), residues: 1582 helix: -2.92 (0.35), residues: 168 sheet: -1.61 (0.39), residues: 168 loop : -3.80 (0.13), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS B 765 PHE 0.015 0.001 PHE I 788 TYR 0.023 0.001 TYR B 861 ARG 0.011 0.001 ARG D 859 *********************** 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 373 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2391 time to fit residues: 130.6215 Evaluate side-chains 291 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1393 ------------------------------------------------------------------------------- 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: 1.9990 chunk 129 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13538 Z= 0.264 Angle : 0.780 8.894 18298 Z= 0.403 Chirality : 0.045 0.173 1918 Planarity : 0.006 0.069 2394 Dihedral : 6.295 22.261 1820 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.17), residues: 1582 helix: -2.89 (0.36), residues: 168 sheet: -1.75 (0.38), residues: 168 loop : -3.77 (0.14), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS D 765 PHE 0.012 0.001 PHE H 788 TYR 0.025 0.001 TYR D 855 ARG 0.010 0.001 ARG D 859 *********************** 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 362 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2405 time to fit residues: 126.4859 Evaluate side-chains 294 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2208 ------------------------------------------------------------------------------- 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: 0.5980 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13538 Z= 0.309 Angle : 0.829 9.060 18298 Z= 0.428 Chirality : 0.045 0.161 1918 Planarity : 0.007 0.100 2394 Dihedral : 6.464 22.438 1820 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.72 % Favored : 80.28 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -4.75 (0.17), residues: 1582 helix: -3.11 (0.33), residues: 182 sheet: -1.74 (0.38), residues: 168 loop : -3.73 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS G 765 PHE 0.016 0.002 PHE J 774 TYR 0.030 0.002 TYR A 861 ARG 0.011 0.001 ARG E 868 ********************** 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 363 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2467 time to fit residues: 129.7127 Evaluate side-chains 297 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2411 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 0.4980 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.3367 r_free = 0.3367 target = 0.075149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069078 restraints weight = 52131.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070723 restraints weight = 29294.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071836 restraints weight = 18437.019| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13538 Z= 0.217 Angle : 0.782 8.990 18298 Z= 0.404 Chirality : 0.046 0.187 1918 Planarity : 0.006 0.072 2394 Dihedral : 6.171 22.211 1820 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.12 % Favored : 83.88 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -4.93 (0.17), residues: 1582 helix: -3.01 (0.33), residues: 168 sheet: -2.99 (0.25), residues: 308 loop : -3.68 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 765 PHE 0.012 0.001 PHE H 788 TYR 0.030 0.001 TYR E 861 ARG 0.009 0.001 ARG C 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.27 seconds wall clock time: 56 minutes 27.21 seconds (3387.21 seconds total)