Starting phenix.real_space_refine on Mon Mar 11 01:25:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7q_15224/03_2024/8a7q_15224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7q_15224/03_2024/8a7q_15224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7q_15224/03_2024/8a7q_15224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7q_15224/03_2024/8a7q_15224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7q_15224/03_2024/8a7q_15224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7q_15224/03_2024/8a7q_15224.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4164 2.51 5 N 1020 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "G" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "H" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "J" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "L" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Time building chain proxies: 3.47, per 1000 atoms: 0.53 Number of scatterers: 6492 At special positions: 0 Unit cell: (147.58, 149.46, 33.84, 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 36 16.00 O 1272 8.00 N 1020 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 80 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 80 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 80 " distance=2.03 Simple disulfide: pdb=" SG CYS J 25 " - pdb=" SG CYS J 80 " distance=2.03 Simple disulfide: pdb=" SG CYS K 25 " - pdb=" SG CYS K 80 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 80 " distance=2.03 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: 1.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.872A pdb=" N ASP E 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP I 34 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.579A pdb=" N VAL A 49 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 49 " --> pdb=" O GLU I 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.989A pdb=" N TYR E 63 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 64 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU E 65 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 66 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR I 63 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 64 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU I 65 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR E 66 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA6, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.003A pdb=" N SER B 33 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU F 36 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 35 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP F 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 37 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER F 33 " --> pdb=" O ASP J 34 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU J 36 " --> pdb=" O SER F 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 35 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP J 38 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL F 37 " --> pdb=" O ASP J 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 53 removed outlier: 9.434A pdb=" N LYS B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N HIS F 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 50 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP F 53 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LYS F 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N HIS J 51 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU F 50 " --> pdb=" O HIS J 51 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ASP J 53 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER F 52 " --> pdb=" O ASP J 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 66 removed outlier: 6.984A pdb=" N TYR F 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR B 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR J 63 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU F 64 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU J 65 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR F 66 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 78 removed outlier: 6.576A pdb=" N GLU B 74 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU F 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 76 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU F 74 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU J 77 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP F 76 " --> pdb=" O GLU J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.184A pdb=" N VAL B 82 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL F 82 " --> pdb=" O ASN J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 22 through 24 removed outlier: 6.739A pdb=" N LEU C 23 " --> pdb=" O ASN G 24 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 39 removed outlier: 6.943A pdb=" N ASP G 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP K 34 " --> pdb=" O SER G 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.533A pdb=" N VAL C 49 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL G 49 " --> pdb=" O GLU K 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.023A pdb=" N TYR G 63 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU C 64 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU G 65 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C 66 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR K 63 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU G 64 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU K 65 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR G 66 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AC2, first strand: chain 'C' and resid 73 through 78 removed outlier: 3.505A pdb=" N GLU G 74 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AC4, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AC5, first strand: chain 'D' and resid 33 through 39 removed outlier: 5.937A pdb=" N SER D 33 " --> pdb=" O ASP H 34 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU H 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 35 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP H 38 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 37 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 33 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLU L 36 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE H 35 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASP L 38 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL H 37 " --> pdb=" O ASP L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.601A pdb=" N VAL D 49 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER H 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS H 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N HIS L 51 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU H 50 " --> pdb=" O HIS L 51 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP L 53 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER H 52 " --> pdb=" O ASP L 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 59 through 66 removed outlier: 6.966A pdb=" N TYR H 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 64 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU H 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR D 66 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR L 63 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU H 64 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU L 65 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR H 66 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 69 through 70 Processing sheet with id=AC9, first strand: chain 'D' and resid 74 through 78 removed outlier: 6.565A pdb=" N GLU D 74 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU H 77 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 76 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU H 74 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU L 77 " --> pdb=" O GLU H 74 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP H 76 " --> pdb=" O GLU L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.088A pdb=" N VAL D 82 " --> pdb=" O ASN H 83 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL H 82 " --> pdb=" O ASN L 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 93 hydrogen bonds defined for protein. 279 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: 1.55 Time building geometry restraints manager: 2.04 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: 1974 1.34 - 1.46: 1269 1.46 - 1.57: 3393 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6684 Sorted by residual: bond pdb=" N GLU G 77 " pdb=" CA GLU G 77 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.23e+00 bond pdb=" N GLU K 77 " pdb=" CA GLU K 77 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N ASP G 76 " pdb=" CA ASP G 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.78e+00 bond pdb=" N GLU I 77 " pdb=" CA GLU I 77 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.68e+00 ... (remaining 6679 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.49: 262 107.49 - 114.12: 3489 114.12 - 120.75: 2836 120.75 - 127.37: 2371 127.37 - 134.00: 78 Bond angle restraints: 9036 Sorted by residual: angle pdb=" CA ASP E 76 " pdb=" CB ASP E 76 " pdb=" CG ASP E 76 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" CA ASP I 76 " pdb=" CB ASP I 76 " pdb=" CG ASP I 76 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASP K 76 " pdb=" CB ASP K 76 " pdb=" CG ASP K 76 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " pdb=" CG ASP A 76 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASP C 76 " pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " ideal model delta sigma weight residual 112.60 116.92 -4.32 1.00e+00 1.00e+00 1.87e+01 ... (remaining 9031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3690 17.02 - 34.05: 189 34.05 - 51.07: 24 51.07 - 68.09: 12 68.09 - 85.12: 9 Dihedral angle restraints: 3924 sinusoidal: 1620 harmonic: 2304 Sorted by residual: dihedral pdb=" CB GLU B 47 " pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " pdb=" OE1 GLU B 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.12 85.12 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CB GLU J 47 " pdb=" CG GLU J 47 " pdb=" CD GLU J 47 " pdb=" OE1 GLU J 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU L 47 " pdb=" CG GLU L 47 " pdb=" CD GLU L 47 " pdb=" OE1 GLU L 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 3921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 635 0.043 - 0.087: 156 0.087 - 0.130: 88 0.130 - 0.174: 23 0.174 - 0.217: 10 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA LYS B 75 " pdb=" N LYS B 75 " pdb=" C LYS B 75 " pdb=" CB LYS B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LYS D 75 " pdb=" N LYS D 75 " pdb=" C LYS D 75 " pdb=" CB LYS D 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LYS J 75 " pdb=" N LYS J 75 " pdb=" C LYS J 75 " pdb=" CB LYS J 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 909 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 70 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C PHE L 70 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE L 70 " -0.007 2.00e-02 2.50e+03 pdb=" N THR L 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 70 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C PHE J 70 " -0.018 2.00e-02 2.50e+03 pdb=" O PHE J 70 " 0.007 2.00e-02 2.50e+03 pdb=" N THR J 71 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 70 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C PHE D 70 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE D 70 " -0.007 2.00e-02 2.50e+03 pdb=" N THR D 71 " -0.006 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 275 2.74 - 3.28: 5580 3.28 - 3.82: 10221 3.82 - 4.36: 12070 4.36 - 4.90: 21788 Nonbonded interactions: 49934 Sorted by model distance: nonbonded pdb=" O LYS D 58 " pdb=" N LYS H 58 " model vdw 2.197 2.520 nonbonded pdb=" O LYS A 58 " pdb=" N LYS E 58 " model vdw 2.229 2.520 nonbonded pdb=" OE2 GLU F 44 " pdb=" NH2 ARG K 45 " model vdw 2.246 2.520 nonbonded pdb=" O LYS F 58 " pdb=" N LYS J 58 " model vdw 2.251 2.520 nonbonded pdb=" O LYS B 58 " pdb=" N LYS F 58 " model vdw 2.252 2.520 ... (remaining 49929 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 6.800 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.980 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.004 0.033 6684 Z= 0.258 Angle : 0.673 4.426 9036 Z= 0.451 Chirality : 0.055 0.217 912 Planarity : 0.003 0.022 1164 Dihedral : 11.640 85.115 2400 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.17), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.13), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 60 HIS 0.004 0.001 HIS L 31 PHE 0.009 0.001 PHE J 70 TYR 0.007 0.001 TYR H 63 ARG 0.001 0.000 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7174 (tmm160) REVERT: B 38 ASP cc_start: 0.7219 (p0) cc_final: 0.6481 (p0) REVERT: C 45 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7093 (tmm160) REVERT: D 38 ASP cc_start: 0.7311 (p0) cc_final: 0.6643 (p0) REVERT: H 38 ASP cc_start: 0.7238 (p0) cc_final: 0.6763 (p0) REVERT: J 27 MET cc_start: 0.7761 (ttt) cc_final: 0.7484 (ttt) REVERT: J 38 ASP cc_start: 0.7302 (p0) cc_final: 0.7083 (p0) REVERT: J 53 ASP cc_start: 0.8012 (t0) cc_final: 0.7677 (t0) REVERT: L 27 MET cc_start: 0.7790 (ttt) cc_final: 0.7503 (ttt) REVERT: L 38 ASP cc_start: 0.7561 (p0) cc_final: 0.7214 (p0) REVERT: L 53 ASP cc_start: 0.8006 (t0) cc_final: 0.7726 (t0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 1.1372 time to fit residues: 448.8298 Evaluate side-chains 293 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 overall best weight: 7.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN B 24 ASN C 83 ASN D 24 ASN F 24 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS H 24 ASN I 24 ASN K 24 ASN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6684 Z= 0.360 Angle : 0.783 7.228 9036 Z= 0.407 Chirality : 0.047 0.145 912 Planarity : 0.004 0.032 1164 Dihedral : 5.056 14.290 840 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.42 % Allowed : 26.23 % Favored : 67.35 % 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: -4.78 (0.18), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.14), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 60 HIS 0.004 0.001 HIS A 31 PHE 0.015 0.002 PHE H 22 TYR 0.019 0.002 TYR B 66 ARG 0.008 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 331 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7198 (tmm160) REVERT: B 41 LYS cc_start: 0.5549 (OUTLIER) cc_final: 0.4796 (pmmt) REVERT: B 48 LYS cc_start: 0.8074 (mttt) cc_final: 0.7752 (pmtt) REVERT: C 44 GLU cc_start: 0.7476 (tt0) cc_final: 0.7266 (tt0) REVERT: C 45 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7151 (tmm160) REVERT: D 41 LYS cc_start: 0.5474 (OUTLIER) cc_final: 0.4687 (pmmt) REVERT: D 48 LYS cc_start: 0.7928 (mttt) cc_final: 0.7713 (pmtt) REVERT: F 74 GLU cc_start: 0.5961 (pp20) cc_final: 0.5666 (pp20) REVERT: I 48 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.4911 (mmpt) REVERT: J 27 MET cc_start: 0.7807 (ttt) cc_final: 0.7542 (ttt) REVERT: K 38 ASP cc_start: 0.6991 (p0) cc_final: 0.6602 (p0) REVERT: K 48 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.4883 (mmpt) REVERT: L 27 MET cc_start: 0.7793 (ttt) cc_final: 0.7525 (ttt) outliers start: 47 outliers final: 15 residues processed: 343 average time/residue: 1.1101 time to fit residues: 399.5831 Evaluate side-chains 309 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 HIS K 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6684 Z= 0.412 Angle : 0.818 11.707 9036 Z= 0.422 Chirality : 0.048 0.185 912 Planarity : 0.004 0.030 1164 Dihedral : 5.325 17.279 840 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 7.92 % Allowed : 26.78 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.19), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 60 HIS 0.005 0.001 HIS A 31 PHE 0.012 0.002 PHE K 22 TYR 0.009 0.001 TYR H 26 ARG 0.008 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 308 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7201 (tmm160) REVERT: B 41 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4323 (mppt) REVERT: B 48 LYS cc_start: 0.8167 (mttt) cc_final: 0.7714 (pmtt) REVERT: C 45 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7202 (tmm160) REVERT: D 41 LYS cc_start: 0.5175 (OUTLIER) cc_final: 0.3820 (pttm) REVERT: D 48 LYS cc_start: 0.7912 (mttt) cc_final: 0.7636 (pmtt) REVERT: E 41 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6633 (tttm) REVERT: F 36 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6656 (tm-30) REVERT: F 38 ASP cc_start: 0.6820 (p0) cc_final: 0.6418 (p0) REVERT: F 47 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: I 38 ASP cc_start: 0.6999 (p0) cc_final: 0.6774 (p0) REVERT: I 48 LYS cc_start: 0.5410 (OUTLIER) cc_final: 0.4422 (mmpt) REVERT: J 27 MET cc_start: 0.7739 (ttt) cc_final: 0.7501 (ttt) REVERT: J 38 ASP cc_start: 0.7525 (p0) cc_final: 0.7208 (p0) REVERT: J 48 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.4863 (mmpt) REVERT: J 76 ASP cc_start: 0.7234 (m-30) cc_final: 0.6839 (m-30) REVERT: K 48 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.4689 (mmpt) REVERT: K 75 LYS cc_start: 0.5078 (mmpt) cc_final: 0.4804 (mmmt) REVERT: L 27 MET cc_start: 0.7759 (ttt) cc_final: 0.7520 (ttt) REVERT: L 38 ASP cc_start: 0.7661 (p0) cc_final: 0.7372 (p0) REVERT: L 48 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.4885 (mmpt) outliers start: 58 outliers final: 25 residues processed: 322 average time/residue: 1.1910 time to fit residues: 401.1433 Evaluate side-chains 309 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6684 Z= 0.299 Angle : 0.786 11.240 9036 Z= 0.398 Chirality : 0.046 0.174 912 Planarity : 0.004 0.037 1164 Dihedral : 5.206 16.450 840 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 7.24 % Allowed : 28.28 % Favored : 64.48 % 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: -4.76 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 60 HIS 0.004 0.001 HIS A 31 PHE 0.015 0.002 PHE L 22 TYR 0.023 0.001 TYR B 66 ARG 0.009 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7155 (tmm160) REVERT: B 48 LYS cc_start: 0.8122 (mttt) cc_final: 0.7596 (pmtt) REVERT: C 45 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7129 (tmm160) REVERT: D 48 LYS cc_start: 0.7798 (mttt) cc_final: 0.7491 (pmtt) REVERT: E 41 LYS cc_start: 0.6796 (tttm) cc_final: 0.6340 (tttm) REVERT: F 47 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5811 (tp30) REVERT: H 73 THR cc_start: 0.8362 (m) cc_final: 0.8047 (m) REVERT: I 48 LYS cc_start: 0.5480 (OUTLIER) cc_final: 0.4389 (mmpt) REVERT: J 27 MET cc_start: 0.7696 (ttt) cc_final: 0.7460 (ttt) REVERT: J 48 LYS cc_start: 0.5708 (OUTLIER) cc_final: 0.4702 (mmpt) REVERT: K 48 LYS cc_start: 0.5628 (OUTLIER) cc_final: 0.4602 (mmpt) REVERT: K 75 LYS cc_start: 0.4949 (mmpt) cc_final: 0.4668 (mmmt) REVERT: L 27 MET cc_start: 0.7708 (ttt) cc_final: 0.7478 (ttt) REVERT: L 48 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.4825 (mmpt) outliers start: 53 outliers final: 32 residues processed: 321 average time/residue: 1.1645 time to fit residues: 391.1577 Evaluate side-chains 317 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 280 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6684 Z= 0.370 Angle : 0.857 12.757 9036 Z= 0.429 Chirality : 0.048 0.171 912 Planarity : 0.004 0.040 1164 Dihedral : 5.399 18.054 840 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 8.74 % Allowed : 28.28 % Favored : 62.98 % 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 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 60 HIS 0.004 0.001 HIS A 31 PHE 0.024 0.002 PHE C 22 TYR 0.011 0.001 TYR E 66 ARG 0.010 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 294 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7166 (tmm160) REVERT: B 41 LYS cc_start: 0.5387 (OUTLIER) cc_final: 0.4530 (pttm) REVERT: B 48 LYS cc_start: 0.8165 (mttt) cc_final: 0.7533 (pmtt) REVERT: C 45 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7122 (tmm160) REVERT: D 41 LYS cc_start: 0.5380 (OUTLIER) cc_final: 0.4726 (pttm) REVERT: D 48 LYS cc_start: 0.7836 (mttt) cc_final: 0.7504 (pmtt) REVERT: E 41 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6379 (tttm) REVERT: I 48 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4045 (mmpt) REVERT: J 27 MET cc_start: 0.7687 (ttt) cc_final: 0.7475 (ttt) REVERT: J 48 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.4793 (mmpt) REVERT: K 48 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.4471 (mmpt) REVERT: K 75 LYS cc_start: 0.4880 (mmpt) cc_final: 0.4635 (mmmt) REVERT: L 27 MET cc_start: 0.7697 (ttt) cc_final: 0.7493 (ttt) REVERT: L 48 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.4848 (mmpt) outliers start: 64 outliers final: 38 residues processed: 316 average time/residue: 1.2214 time to fit residues: 403.6661 Evaluate side-chains 318 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 273 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6684 Z= 0.307 Angle : 0.888 14.910 9036 Z= 0.433 Chirality : 0.048 0.283 912 Planarity : 0.004 0.040 1164 Dihedral : 5.370 21.087 840 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 7.51 % Allowed : 28.42 % Favored : 64.07 % 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: -4.76 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 60 HIS 0.003 0.001 HIS A 31 PHE 0.015 0.001 PHE L 22 TYR 0.024 0.001 TYR B 66 ARG 0.010 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 299 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7089 (tmm160) REVERT: B 41 LYS cc_start: 0.5462 (OUTLIER) cc_final: 0.4817 (pttm) REVERT: B 48 LYS cc_start: 0.8101 (mttt) cc_final: 0.7326 (pmtt) REVERT: B 58 LYS cc_start: 0.4341 (OUTLIER) cc_final: 0.3791 (pmtt) REVERT: D 41 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4692 (pttm) REVERT: D 48 LYS cc_start: 0.7724 (mttt) cc_final: 0.7410 (pmtt) REVERT: I 48 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.4242 (mmpt) REVERT: J 27 MET cc_start: 0.7665 (ttt) cc_final: 0.7461 (ttt) REVERT: J 48 LYS cc_start: 0.5841 (OUTLIER) cc_final: 0.4936 (mmpt) REVERT: K 48 LYS cc_start: 0.5454 (OUTLIER) cc_final: 0.4400 (mmpt) REVERT: L 27 MET cc_start: 0.7670 (ttt) cc_final: 0.7456 (ttt) REVERT: L 48 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.4849 (mmpt) outliers start: 55 outliers final: 34 residues processed: 318 average time/residue: 1.2647 time to fit residues: 419.5676 Evaluate side-chains 320 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6684 Z= 0.314 Angle : 0.957 14.799 9036 Z= 0.462 Chirality : 0.047 0.168 912 Planarity : 0.004 0.044 1164 Dihedral : 5.450 21.755 840 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 6.28 % Allowed : 33.33 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 60 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.001 PHE A 22 TYR 0.024 0.001 TYR C 66 ARG 0.010 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 289 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7141 (tmm160) REVERT: B 41 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.4828 (pttm) REVERT: B 48 LYS cc_start: 0.8052 (mttt) cc_final: 0.7320 (OUTLIER) REVERT: B 58 LYS cc_start: 0.4645 (OUTLIER) cc_final: 0.4056 (pmtt) REVERT: C 45 ARG cc_start: 0.6268 (ppt90) cc_final: 0.5346 (pmt-80) REVERT: D 41 LYS cc_start: 0.5344 (OUTLIER) cc_final: 0.4688 (pttm) REVERT: D 48 LYS cc_start: 0.7733 (mttt) cc_final: 0.7378 (pmtt) REVERT: I 48 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.4212 (mmpt) REVERT: J 48 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.4664 (mmpt) REVERT: K 48 LYS cc_start: 0.5457 (OUTLIER) cc_final: 0.4409 (mmpt) REVERT: K 75 LYS cc_start: 0.4864 (OUTLIER) cc_final: 0.3825 (mmpt) REVERT: L 48 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5028 (mmpt) outliers start: 46 outliers final: 29 residues processed: 304 average time/residue: 1.2061 time to fit residues: 382.9954 Evaluate side-chains 313 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 277 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN L 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6684 Z= 0.277 Angle : 0.971 15.128 9036 Z= 0.467 Chirality : 0.048 0.175 912 Planarity : 0.004 0.047 1164 Dihedral : 5.450 21.654 840 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.46 % Allowed : 35.11 % Favored : 59.43 % 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: -4.85 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP I 60 HIS 0.003 0.001 HIS A 31 PHE 0.015 0.001 PHE L 22 TYR 0.023 0.001 TYR D 66 ARG 0.011 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 292 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7122 (tmm160) REVERT: B 41 LYS cc_start: 0.5605 (OUTLIER) cc_final: 0.4951 (pttm) REVERT: B 47 GLU cc_start: 0.5206 (pm20) cc_final: 0.4968 (pm20) REVERT: B 48 LYS cc_start: 0.7910 (mttt) cc_final: 0.7239 (pptt) REVERT: B 58 LYS cc_start: 0.4630 (OUTLIER) cc_final: 0.4092 (pmtt) REVERT: C 45 ARG cc_start: 0.6098 (ppt90) cc_final: 0.5316 (pmt-80) REVERT: D 41 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.4614 (pttm) REVERT: D 48 LYS cc_start: 0.7662 (mttt) cc_final: 0.7415 (pmtt) REVERT: I 48 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.5081 (mmpt) REVERT: J 48 LYS cc_start: 0.5602 (OUTLIER) cc_final: 0.4749 (mmpt) REVERT: K 48 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.4501 (mmpt) REVERT: K 76 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6816 (m-30) REVERT: L 48 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.4981 (mmpt) outliers start: 40 outliers final: 27 residues processed: 305 average time/residue: 1.1000 time to fit residues: 351.3719 Evaluate side-chains 315 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 280 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.7324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6684 Z= 0.297 Angle : 1.035 15.451 9036 Z= 0.493 Chirality : 0.048 0.234 912 Planarity : 0.004 0.049 1164 Dihedral : 5.439 21.010 840 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 6.01 % Allowed : 35.38 % Favored : 58.61 % 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: -4.89 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP I 60 HIS 0.003 0.001 HIS A 31 PHE 0.023 0.001 PHE A 22 TYR 0.022 0.001 TYR C 66 ARG 0.011 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 285 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7155 (tmm160) REVERT: A 76 ASP cc_start: 0.6549 (m-30) cc_final: 0.5967 (m-30) REVERT: B 41 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.4888 (pttm) REVERT: B 58 LYS cc_start: 0.4526 (OUTLIER) cc_final: 0.3989 (pmtt) REVERT: C 45 ARG cc_start: 0.6341 (ppt90) cc_final: 0.5967 (ptm-80) REVERT: D 41 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.4518 (pttm) REVERT: D 48 LYS cc_start: 0.7726 (mttt) cc_final: 0.7510 (pmtt) REVERT: K 48 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.4607 (mmpt) REVERT: K 75 LYS cc_start: 0.4868 (OUTLIER) cc_final: 0.3769 (mmpt) REVERT: K 76 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6856 (m-30) outliers start: 44 outliers final: 26 residues processed: 299 average time/residue: 1.1136 time to fit residues: 349.0537 Evaluate side-chains 312 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 280 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain L residue 38 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6684 Z= 0.404 Angle : 1.095 14.992 9036 Z= 0.527 Chirality : 0.050 0.226 912 Planarity : 0.004 0.051 1164 Dihedral : 5.830 22.597 840 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 5.33 % Allowed : 36.75 % Favored : 57.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 60 HIS 0.003 0.001 HIS L 31 PHE 0.016 0.002 PHE J 22 TYR 0.022 0.001 TYR D 66 ARG 0.011 0.001 ARG E 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 270 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7131 (tmm160) REVERT: B 48 LYS cc_start: 0.7919 (mttt) cc_final: 0.7125 (pmtt) REVERT: C 45 ARG cc_start: 0.6256 (ppt90) cc_final: 0.5178 (pmt-80) REVERT: D 41 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.4693 (pttm) REVERT: E 50 GLU cc_start: 0.7240 (mp0) cc_final: 0.6690 (mp0) REVERT: K 48 LYS cc_start: 0.5567 (OUTLIER) cc_final: 0.4586 (mmpt) REVERT: K 75 LYS cc_start: 0.4849 (OUTLIER) cc_final: 0.4624 (mmmt) outliers start: 39 outliers final: 30 residues processed: 287 average time/residue: 1.1018 time to fit residues: 331.3291 Evaluate side-chains 302 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 269 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 76 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 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 = 0.4305 r_free = 0.4305 target = 0.106566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.100362 restraints weight = 20963.479| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.78 r_work: 0.4086 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.7599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6684 Z= 0.278 Angle : 1.066 15.988 9036 Z= 0.508 Chirality : 0.049 0.257 912 Planarity : 0.004 0.051 1164 Dihedral : 5.570 20.819 840 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.14 % Allowed : 39.62 % Favored : 57.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 60 HIS 0.003 0.001 HIS E 31 PHE 0.009 0.001 PHE D 22 TYR 0.012 0.001 TYR K 66 ARG 0.011 0.001 ARG E 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5137.00 seconds wall clock time: 90 minutes 43.15 seconds (5443.15 seconds total)