Starting phenix.real_space_refine (version: dev) on Tue Dec 13 01:43:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2022/6oks_20103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_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_20103/12_2022/6oks_20103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2022/6oks_20103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_2022/6oks_20103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oks_20103/12_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-4807/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: 7.49, 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: 4.89 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: 0.59 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: 3.03 Time building geometry restraints manager: 5.31 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.710 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 33.350 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.980 ------------------------------------------------------------------------------- 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 : 1.642 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: 0.2408 time to fit residues: 201.3489 Evaluate side-chains 313 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 288 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1075 time to fit residues: 7.1930 ------------------------------------------------------------------------------- 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: 0.0870 chunk 139 optimal weight: 1.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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** N 792 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13538 Z= 0.216 Angle : 0.701 6.343 18298 Z= 0.365 Chirality : 0.042 0.164 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.687 23.461 1820 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % 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: -5.50 (0.15), residues: 1582 helix: -4.50 (0.17), residues: 182 sheet: -2.06 (0.38), residues: 168 loop : -4.15 (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 436 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 431 time to evaluate : 1.605 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: 436 average time/residue: 0.2432 time to fit residues: 152.5399 Evaluate side-chains 300 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0782 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 0.0070 chunk 38 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 124 optimal weight: 0.0980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.6204 ------------------------------------------------------------------------------- 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 759 GLN ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 13538 Z= 0.333 Angle : 0.769 6.695 18298 Z= 0.403 Chirality : 0.043 0.146 1918 Planarity : 0.007 0.071 2394 Dihedral : 6.746 22.299 1820 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.88 % Favored : 83.12 % 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: -5.41 (0.15), residues: 1582 helix: -4.08 (0.24), residues: 182 sheet: -1.76 (0.40), residues: 168 loop : -4.19 (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 379 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 1.798 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: 0 residues processed: 379 average time/residue: 0.2282 time to fit residues: 125.8651 Evaluate side-chains 290 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1389 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 838 ASN ** 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 794 ASN ** 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: 0.8055 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13538 Z= 0.191 Angle : 0.683 7.521 18298 Z= 0.354 Chirality : 0.043 0.154 1918 Planarity : 0.006 0.066 2394 Dihedral : 6.290 23.850 1820 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % 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: -5.22 (0.15), residues: 1582 helix: -3.71 (0.27), residues: 168 sheet: -1.62 (0.40), residues: 168 loop : -4.10 (0.12), residues: 1246 *********************** 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 402 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.2468 time to fit residues: 141.2200 Evaluate side-chains 303 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3399 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 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: 0.8129 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13538 Z= 0.328 Angle : 0.763 7.596 18298 Z= 0.398 Chirality : 0.044 0.135 1918 Planarity : 0.007 0.073 2394 Dihedral : 6.482 21.895 1820 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.13 % Favored : 82.87 % 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: -5.14 (0.16), residues: 1582 helix: -3.54 (0.28), residues: 182 sheet: -1.65 (0.39), residues: 168 loop : -4.05 (0.13), residues: 1232 *********************** 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 381 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 1.589 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: 381 average time/residue: 0.2414 time to fit residues: 132.7708 Evaluate side-chains 292 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0709 ------------------------------------------------------------------------------- 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: 8.9990 chunk 134 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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: 0.8079 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 13538 Z= 0.200 Angle : 0.703 8.202 18298 Z= 0.361 Chirality : 0.043 0.207 1918 Planarity : 0.006 0.070 2394 Dihedral : 6.214 23.161 1820 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.03 % Favored : 85.97 % 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: -5.26 (0.16), residues: 1582 helix: -3.41 (0.30), residues: 182 sheet: -3.12 (0.26), residues: 308 loop : -3.90 (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 388 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 387 time to evaluate : 1.769 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: 1 outliers final: 0 residues processed: 388 average time/residue: 0.2415 time to fit residues: 134.2225 Evaluate side-chains 308 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0296 ------------------------------------------------------------------------------- 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: 0.0020 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 91 optimal weight: 0.0570 overall best weight: 2.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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: 0.8088 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13538 Z= 0.226 Angle : 0.727 8.091 18298 Z= 0.374 Chirality : 0.044 0.191 1918 Planarity : 0.006 0.070 2394 Dihedral : 6.127 21.900 1820 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.31 % Favored : 83.69 % 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: -4.93 (0.16), residues: 1582 helix: -3.26 (0.30), residues: 182 sheet: -1.77 (0.39), residues: 168 loop : -3.87 (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 381 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.2311 time to fit residues: 127.8451 Evaluate side-chains 304 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2544 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 851 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 13538 Z= 0.320 Angle : 0.803 8.234 18298 Z= 0.417 Chirality : 0.045 0.200 1918 Planarity : 0.007 0.066 2394 Dihedral : 6.420 22.497 1820 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.02 % Favored : 81.98 % 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: -4.90 (0.17), residues: 1582 helix: -3.16 (0.31), residues: 182 sheet: -1.88 (0.38), residues: 168 loop : -3.84 (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 369 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 369 average time/residue: 0.2290 time to fit residues: 123.4193 Evaluate side-chains 301 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1100 time to fit residues: 2.3982 ------------------------------------------------------------------------------- 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: 0.9990 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 0.0570 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.6142 ------------------------------------------------------------------------------- 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** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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: 0.8083 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 13538 Z= 0.222 Angle : 0.762 9.425 18298 Z= 0.392 Chirality : 0.045 0.251 1918 Planarity : 0.006 0.068 2394 Dihedral : 6.198 25.822 1820 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.25 % Favored : 83.75 % 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: -4.78 (0.17), residues: 1582 helix: -3.12 (0.32), residues: 182 sheet: -1.88 (0.38), residues: 168 loop : -3.72 (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 380 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.645 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: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2434 time to fit residues: 134.8564 Evaluate side-chains 306 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3343 ------------------------------------------------------------------------------- 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: 8.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- 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** ** G 838 ASN ** 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: 0.8089 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 13538 Z= 0.231 Angle : 0.788 8.445 18298 Z= 0.405 Chirality : 0.045 0.230 1918 Planarity : 0.007 0.090 2394 Dihedral : 6.161 25.072 1820 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.69 % Favored : 83.31 % 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: -4.74 (0.17), residues: 1582 helix: -3.12 (0.32), residues: 182 sheet: -1.99 (0.38), residues: 168 loop : -3.67 (0.14), residues: 1232 ********************** 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 370 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.566 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: 370 average time/residue: 0.2357 time to fit residues: 125.9639 Evaluate side-chains 307 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.619 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1032 ------------------------------------------------------------------------------- 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: 0.0170 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.075211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069083 restraints weight = 53014.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070722 restraints weight = 29891.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071863 restraints weight = 18854.305| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 13538 Z= 0.260 Angle : 0.807 9.568 18298 Z= 0.417 Chirality : 0.045 0.251 1918 Planarity : 0.007 0.119 2394 Dihedral : 6.228 25.159 1820 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.64 % Favored : 82.36 % 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: -4.73 (0.17), residues: 1582 helix: -3.06 (0.33), residues: 182 sheet: -2.06 (0.38), residues: 168 loop : -3.66 (0.14), residues: 1232 =============================================================================== Job complete usr+sys time: 2867.60 seconds wall clock time: 53 minutes 2.02 seconds (3182.02 seconds total)