Starting phenix.real_space_refine (version: dev) on Tue Apr 5 11:42:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/04_2022/6oks_20103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/04_2022/6oks_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_20103/04_2022/6oks_20103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/04_2022/6oks_20103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/04_2022/6oks_20103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/04_2022/6oks_20103.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: 7.53, per 1000 atoms: 0.57 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: 5.34 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: 0.69 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: 3.31 Time building geometry restraints manager: 5.78 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 4.550 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.120 Process input model: 35.130 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 % 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 *********************** 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 : 1.710 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 outliers start: 140 outliers final: 25 residues processed: 589 average time/residue: 0.2423 time to fit residues: 203.2892 Evaluate side-chains 312 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 287 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1084 time to fit residues: 7.3741 ------------------------------------------------------------------------------- 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: 4.9990 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** 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 792 GLN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 13538 Z= 0.231 Angle : 0.717 7.997 18298 Z= 0.375 Chirality : 0.042 0.168 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.721 23.507 1820 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer Outliers : 0.35 % 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: -5.51 (0.15), residues: 1582 helix: -4.50 (0.17), residues: 182 sheet: -2.01 (0.38), residues: 168 loop : -4.17 (0.12), residues: 1232 *********************** 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 433 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 428 time to evaluate : 1.746 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 outliers start: 5 outliers final: 0 residues processed: 433 average time/residue: 0.2432 time to fit residues: 151.8328 Evaluate side-chains 299 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2373 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 0.0570 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.6106 ------------------------------------------------------------------------------- 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 802 GLN ** 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 794 ASN ** 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** ** N 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.107 13538 Z= 0.421 Angle : 0.873 10.203 18298 Z= 0.456 Chirality : 0.046 0.147 1918 Planarity : 0.007 0.074 2394 Dihedral : 7.103 24.464 1820 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.15), residues: 1582 helix: -3.99 (0.24), residues: 182 sheet: -1.78 (0.39), residues: 168 loop : -4.20 (0.12), residues: 1232 *********************** 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 368 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 366 time to evaluate : 1.719 Fit side-chains 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: 368 average time/residue: 0.2337 time to fit residues: 125.8645 Evaluate side-chains 273 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1489 ------------------------------------------------------------------------------- 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: 8.9990 chunk 105 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 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 802 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 794 ASN ** M 802 GLN ** 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: 0.8181 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.092 13538 Z= 0.361 Angle : 0.828 8.563 18298 Z= 0.434 Chirality : 0.045 0.129 1918 Planarity : 0.007 0.072 2394 Dihedral : 7.002 23.026 1820 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer Outliers : 0.07 % 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: -5.54 (0.16), residues: 1582 helix: -3.54 (0.28), residues: 182 sheet: -3.22 (0.26), residues: 308 loop : -4.15 (0.14), residues: 1092 *********************** 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 379 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 1.739 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 outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.2617 time to fit residues: 142.3015 Evaluate side-chains 275 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2744 ------------------------------------------------------------------------------- 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: 0.3980 chunk 84 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.2964 ------------------------------------------------------------------------------- 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 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 765 HIS M 794 ASN ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.160 13538 Z= 0.336 Angle : 0.800 10.133 18298 Z= 0.417 Chirality : 0.044 0.135 1918 Planarity : 0.007 0.071 2394 Dihedral : 6.793 22.274 1820 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer Outliers : 0.07 % 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 (0.16), residues: 1582 helix: -3.30 (0.31), residues: 182 sheet: -3.20 (0.26), residues: 308 loop : -4.05 (0.14), residues: 1092 *********************** 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 376 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 1.726 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 outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.2477 time to fit residues: 134.3400 Evaluate side-chains 286 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3241 ------------------------------------------------------------------------------- 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: 2.9990 chunk 134 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 123 optimal weight: 0.0040 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- 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** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN ** 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: 0.8092 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.149 13538 Z= 0.199 Angle : 0.729 12.471 18298 Z= 0.376 Chirality : 0.043 0.205 1918 Planarity : 0.006 0.065 2394 Dihedral : 6.322 23.311 1820 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Rotamer Outliers : 0.07 % 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 (0.17), residues: 1582 helix: -3.16 (0.32), residues: 182 sheet: -3.14 (0.26), residues: 308 loop : -3.89 (0.14), residues: 1092 *********************** 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 387 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 386 time to evaluate : 1.691 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 outliers start: 1 outliers final: 1 residues processed: 387 average time/residue: 0.2602 time to fit residues: 143.1520 Evaluate side-chains 311 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1214 time to fit residues: 2.4572 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 148 optimal weight: 0.0670 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 91 optimal weight: 0.0470 overall best weight: 2.2222 ------------------------------------------------------------------------------- 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** I 802 GLN ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN M 802 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: 0.8116 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.268 13538 Z= 0.338 Angle : 0.785 16.714 18298 Z= 0.412 Chirality : 0.044 0.211 1918 Planarity : 0.007 0.123 2394 Dihedral : 6.304 21.887 1820 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer Outliers : 0.00 % 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: -3.02 (0.33), residues: 182 sheet: -1.54 (0.40), residues: 168 loop : -3.86 (0.13), residues: 1232 *********************** 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 375 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.772 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: 375 average time/residue: 0.2628 time to fit residues: 140.5632 Evaluate side-chains 295 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2937 ------------------------------------------------------------------------------- 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: 8.9990 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 13 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 135 optimal weight: 0.5980 overall best weight: 3.2184 ------------------------------------------------------------------------------- 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** N 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.401 13538 Z= 0.338 Angle : 0.836 21.759 18298 Z= 0.438 Chirality : 0.045 0.181 1918 Planarity : 0.007 0.066 2394 Dihedral : 6.544 22.791 1820 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.65 % Favored : 81.35 % Rotamer Outliers : 0.00 % 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: -4.80 (0.17), residues: 1582 helix: -3.11 (0.32), residues: 182 sheet: -1.62 (0.40), residues: 168 loop : -3.79 (0.14), residues: 1232 *********************** 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 365 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.766 Fit side-chains 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: 365 average time/residue: 0.2458 time to fit residues: 129.7416 Evaluate side-chains 295 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2962 ------------------------------------------------------------------------------- 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: 0.1980 chunk 129 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.8544 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.021 13538 Z= 0.462 Angle : 1.180 106.049 18298 Z= 0.524 Chirality : 0.045 0.268 1918 Planarity : 0.007 0.082 2394 Dihedral : 6.516 22.630 1820 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.02 % Favored : 81.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % 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: -3.10 (0.32), residues: 182 sheet: -1.58 (0.40), residues: 168 loop : -3.75 (0.14), residues: 1232 *********************** 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 356 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.684 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: 356 average time/residue: 0.2321 time to fit residues: 120.6107 Evaluate side-chains 292 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2300 ------------------------------------------------------------------------------- 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: 0.8980 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 chunk 101 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.824 13538 Z= 0.328 Angle : 1.025 80.422 18298 Z= 0.473 Chirality : 0.044 0.185 1918 Planarity : 0.006 0.068 2394 Dihedral : 6.109 22.939 1820 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer Outliers : 0.00 % 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: -4.88 (0.17), residues: 1582 helix: -2.94 (0.34), residues: 168 sheet: -2.93 (0.27), residues: 308 loop : -3.65 (0.15), residues: 1106 ********************** 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 396 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.747 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: 396 average time/residue: 0.2414 time to fit residues: 139.0084 Evaluate side-chains 319 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3370 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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** ** N 802 GLN ** 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 = 0.3332 r_free = 0.3332 target = 0.073610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067387 restraints weight = 52627.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069022 restraints weight = 29885.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070147 restraints weight = 19119.386| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.814 13538 Z= 0.397 Angle : 1.059 79.277 18298 Z= 0.501 Chirality : 0.045 0.176 1918 Planarity : 0.007 0.089 2394 Dihedral : 6.308 22.014 1820 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.15 % Favored : 80.85 % Rotamer Outliers : 0.00 % 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: -4.61 (0.17), residues: 1582 helix: -2.76 (0.36), residues: 168 sheet: -1.70 (0.40), residues: 168 loop : -3.65 (0.14), residues: 1246 =============================================================================== Job complete usr+sys time: 2944.60 seconds wall clock time: 54 minutes 22.25 seconds (3262.25 seconds total)