Starting phenix.real_space_refine on Mon Feb 19 15:08:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1e_15073/02_2024/8a1e_15073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1e_15073/02_2024/8a1e_15073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1e_15073/02_2024/8a1e_15073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1e_15073/02_2024/8a1e_15073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1e_15073/02_2024/8a1e_15073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1e_15073/02_2024/8a1e_15073.pdb" } resolution = 2.83 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= -0.000 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6654 atoms to isotropic. 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 123 5.16 5 C 11655 2.51 5 N 3150 2.21 5 O 3474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 368": "OD1" <-> "OD2" Residue "L TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18402 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 bond proxies already assigned to first conformer: 2736 Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 827 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "B" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "F" Number of atoms: 2686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 bond proxies already assigned to first conformer: 2736 Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 827 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "J" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "K" Number of atoms: 2686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 bond proxies already assigned to first conformer: 2736 Chain: "L" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "M" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 827 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Chain: "N" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "O" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Time building chain proxies: 13.20, per 1000 atoms: 0.72 Number of scatterers: 18402 At special positions: 0 Unit cell: (160.06, 161.12, 96.46, 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 123 16.00 O 3474 8.00 N 3150 7.00 C 11655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 252 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 283 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 189 " - pdb=" SG CYS F 228 " distance=2.03 Simple disulfide: pdb=" SG CYS F 223 " - pdb=" SG CYS F 252 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 351 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 283 " distance=2.03 Simple disulfide: pdb=" SG CYS K 35 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 94 " distance=2.03 Simple disulfide: pdb=" SG CYS K 159 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 189 " - pdb=" SG CYS K 228 " distance=2.03 Simple disulfide: pdb=" SG CYS K 223 " - pdb=" SG CYS K 252 " distance=2.04 Simple disulfide: pdb=" SG CYS K 344 " - pdb=" SG CYS K 351 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " 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: 6.47 Conformation dependent library (CDL) restraints added in 5.0 seconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 57 sheets defined 11.1% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.560A pdb=" N LEU A 22 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.818A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.611A pdb=" N ASN A 259 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 294 removed outlier: 3.781A pdb=" N GLU A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR D 91 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.185A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.560A pdb=" N LEU F 22 " --> pdb=" O ILE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.818A pdb=" N ALA F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.611A pdb=" N ASN F 259 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 294 removed outlier: 3.781A pdb=" N GLU F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 373 through 380 Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR G 91 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.185A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'K' and resid 18 through 22 removed outlier: 3.560A pdb=" N LEU K 22 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.818A pdb=" N ALA K 103 " --> pdb=" O ASN K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.611A pdb=" N ASN K 259 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 294 removed outlier: 3.781A pdb=" N GLU K 275 " --> pdb=" O LEU K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 302 Processing helix chain 'K' and resid 303 through 305 No H-bonds generated for 'chain 'K' and resid 303 through 305' Processing helix chain 'K' and resid 373 through 380 Processing helix chain 'K' and resid 384 through 388 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR L 91 " --> pdb=" O THR L 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.186A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing sheet with id= 1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 322 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 38 through 46 Processing sheet with id= 4, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.875A pdb=" N ILE A 177 " --> pdb=" O CYS A 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 178 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS A 169 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 223 through 227 Processing sheet with id= 6, first strand: chain 'A' and resid 295 through 296 Processing sheet with id= 7, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.648A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= 9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.950A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.773A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.633A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 10 through 13 Processing sheet with id= 14, first strand: chain 'C' and resid 4 through 5 Processing sheet with id= 15, first strand: chain 'C' and resid 19 through 22 removed outlier: 4.062A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 65 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 74 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.490A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 9 through 10 removed outlier: 6.585A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 40 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 45 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.504A pdb=" N VAL B 110 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR F 5 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS F 328 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU F 11 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP F 326 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU F 322 " --> pdb=" O ILE F 17 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR F 5 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS F 328 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU F 11 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP F 326 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 38 through 46 Processing sheet with id= 23, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.875A pdb=" N ILE F 177 " --> pdb=" O CYS F 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP F 178 " --> pdb=" O CYS F 169 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS F 169 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'F' and resid 223 through 227 Processing sheet with id= 25, first strand: chain 'F' and resid 295 through 296 Processing sheet with id= 26, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.648A pdb=" N ILE F 363 " --> pdb=" O PHE F 359 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= 28, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.950A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.774A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.633A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'H' and resid 10 through 13 Processing sheet with id= 33, first strand: chain 'I' and resid 4 through 5 Processing sheet with id= 34, first strand: chain 'I' and resid 19 through 22 removed outlier: 4.062A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 72 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER I 65 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR I 74 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 18 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.585A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG J 40 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE J 45 " --> pdb=" O ARG J 40 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'J' and resid 9 through 10 removed outlier: 3.503A pdb=" N VAL J 110 " --> pdb=" O ILE J 98 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'K' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR K 5 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS K 328 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU K 11 " --> pdb=" O ASP K 326 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP K 326 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU K 322 " --> pdb=" O ILE K 17 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'K' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR K 5 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS K 328 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU K 11 " --> pdb=" O ASP K 326 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP K 326 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K' and resid 38 through 46 Processing sheet with id= 42, first strand: chain 'K' and resid 59 through 61 removed outlier: 3.875A pdb=" N ILE K 177 " --> pdb=" O CYS K 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP K 178 " --> pdb=" O CYS K 169 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS K 169 " --> pdb=" O TRP K 178 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'K' and resid 223 through 227 Processing sheet with id= 44, first strand: chain 'K' and resid 295 through 296 Processing sheet with id= 45, first strand: chain 'K' and resid 358 through 360 removed outlier: 6.648A pdb=" N ILE K 363 " --> pdb=" O PHE K 359 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'L' and resid 3 through 7 Processing sheet with id= 47, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.951A pdb=" N MET L 34 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.774A pdb=" N TYR L 108 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.633A pdb=" N SER M 22 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'M' and resid 10 through 13 Processing sheet with id= 52, first strand: chain 'N' and resid 4 through 5 Processing sheet with id= 53, first strand: chain 'N' and resid 19 through 22 removed outlier: 4.062A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR N 74 " --> pdb=" O THR N 63 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.489A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'O' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET O 18 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'O' and resid 9 through 10 removed outlier: 6.585A pdb=" N LYS O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP O 47 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG O 40 " --> pdb=" O PHE O 45 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE O 45 " --> pdb=" O ARG O 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 9 through 10 removed outlier: 3.504A pdb=" N VAL O 110 " --> pdb=" O ILE O 98 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1554 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: 6.98 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5907 1.34 - 1.46: 4720 1.46 - 1.58: 8054 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 18861 Sorted by residual: bond pdb=" CG1 ILE K 339 " pdb=" CD1 ILE K 339 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.76e-01 bond pdb=" CG1 ILE F 339 " pdb=" CD1 ILE F 339 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.69e-01 bond pdb=" CG1 ILE A 339 " pdb=" CD1 ILE A 339 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.57e-01 bond pdb=" CA THR F 90 " pdb=" CB THR F 90 " ideal model delta sigma weight residual 1.526 1.538 -0.012 1.51e-02 4.39e+03 6.42e-01 bond pdb=" CB PRO E 95 " pdb=" CG PRO E 95 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.34e-01 ... (remaining 18856 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.52: 654 106.52 - 113.39: 10070 113.39 - 120.26: 6383 120.26 - 127.14: 8203 127.14 - 134.01: 256 Bond angle restraints: 25566 Sorted by residual: angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 112.96 109.95 3.01 1.00e+00 1.00e+00 9.08e+00 angle pdb=" N VAL D 64 " pdb=" CA VAL D 64 " pdb=" C VAL D 64 " ideal model delta sigma weight residual 112.96 109.96 3.00 1.00e+00 1.00e+00 8.98e+00 angle pdb=" N VAL L 64 " pdb=" CA VAL L 64 " pdb=" C VAL L 64 " ideal model delta sigma weight residual 112.96 109.99 2.97 1.00e+00 1.00e+00 8.81e+00 angle pdb=" C SER C 50 " pdb=" N ALA C 51 " pdb=" CA ALA C 51 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.01e+00 angle pdb=" C SER I 50 " pdb=" N ALA I 51 " pdb=" CA ALA I 51 " ideal model delta sigma weight residual 121.54 126.92 -5.38 1.91e+00 2.74e-01 7.92e+00 ... (remaining 25561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 10167 17.27 - 34.54: 861 34.54 - 51.81: 177 51.81 - 69.07: 30 69.07 - 86.34: 9 Dihedral angle restraints: 11244 sinusoidal: 4458 harmonic: 6786 Sorted by residual: dihedral pdb=" CB CYS F 35 " pdb=" SG CYS F 35 " pdb=" SG CYS F 207 " pdb=" CB CYS F 207 " ideal model delta sinusoidal sigma weight residual 93.00 179.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 179.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS K 35 " pdb=" SG CYS K 35 " pdb=" SG CYS K 207 " pdb=" CB CYS K 207 " ideal model delta sinusoidal sigma weight residual 93.00 179.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 ... (remaining 11241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1597 0.028 - 0.056: 753 0.056 - 0.084: 216 0.084 - 0.111: 182 0.111 - 0.139: 36 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA ILE K 373 " pdb=" N ILE K 373 " pdb=" C ILE K 373 " pdb=" CB ILE K 373 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE F 373 " pdb=" N ILE F 373 " pdb=" C ILE F 373 " pdb=" CB ILE F 373 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 373 " pdb=" N ILE A 373 " pdb=" C ILE A 373 " pdb=" CB ILE A 373 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2781 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 90 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO F 91 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 91 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 91 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 90 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO A 91 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 90 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO K 91 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 91 " 0.024 5.00e-02 4.00e+02 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 51 2.30 - 2.95: 8256 2.95 - 3.60: 25729 3.60 - 4.25: 44067 4.25 - 4.90: 75615 Nonbonded interactions: 153718 Sorted by model distance: nonbonded pdb=" SD MET A 291 " pdb=" CE MET F 385 " model vdw 1.655 3.820 nonbonded pdb=" SD MET F 291 " pdb=" CE MET K 385 " model vdw 1.655 3.820 nonbonded pdb=" CE MET A 385 " pdb=" SD MET K 291 " model vdw 1.655 3.820 nonbonded pdb=" O SER A 379 " pdb=" NH1 ARG K 264 " model vdw 1.826 2.520 nonbonded pdb=" NH1 ARG A 264 " pdb=" O SER F 379 " model vdw 1.827 2.520 ... (remaining 153713 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' and (resid 1 through 233 or resid 235 through 399)) selection = (chain 'F' and (resid 1 through 233 or resid 235 through 399)) selection = (chain 'K' and (resid 1 through 233 or resid 235 through 399)) } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } 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=0.50 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 14.660 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 56.190 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.003 0.033 18861 Z= 0.213 Angle : 0.539 6.587 25566 Z= 0.287 Chirality : 0.042 0.139 2784 Planarity : 0.004 0.043 3264 Dihedral : 12.784 82.462 6807 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.52 (0.17), residues: 2325 helix: 0.13 (0.39), residues: 159 sheet: -0.26 (0.19), residues: 720 loop : -0.38 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 109 HIS 0.003 0.001 HIS N 91 PHE 0.009 0.001 PHE J 45 TYR 0.013 0.001 TYR D 105 ARG 0.003 0.000 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.8822 (tt) cc_final: 0.8620 (tm) REVERT: B 34 MET cc_start: 0.7402 (tpp) cc_final: 0.7155 (tpp) REVERT: F 44 MET cc_start: 0.8828 (mtm) cc_final: 0.8558 (mtm) REVERT: F 376 MET cc_start: 0.9136 (ttp) cc_final: 0.8828 (ttm) REVERT: I 87 TYR cc_start: 0.7932 (m-80) cc_final: 0.7710 (m-80) REVERT: J 34 MET cc_start: 0.7333 (tpp) cc_final: 0.7034 (tpp) REVERT: K 278 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8171 (tttp) REVERT: K 376 MET cc_start: 0.9049 (ttp) cc_final: 0.8634 (ttm) REVERT: N 4 MET cc_start: 0.7571 (mmt) cc_final: 0.7238 (mmt) REVERT: O 34 MET cc_start: 0.7391 (tpp) cc_final: 0.7162 (tpp) REVERT: O 94 TYR cc_start: 0.7746 (m-10) cc_final: 0.7277 (m-10) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 1.0204 time to fit residues: 336.9179 Evaluate side-chains 247 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS E 93 ASN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 HIS F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 261 HIS K 356 ASN M 93 ASN N 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18861 Z= 0.228 Angle : 0.578 9.087 25566 Z= 0.295 Chirality : 0.043 0.182 2784 Planarity : 0.004 0.042 3264 Dihedral : 4.770 24.782 2565 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.13 % Allowed : 9.07 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.48 (0.17), residues: 2325 helix: 0.11 (0.40), residues: 159 sheet: 0.01 (0.19), residues: 687 loop : -0.49 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 36 HIS 0.010 0.001 HIS F 150 PHE 0.010 0.001 PHE G 95 TYR 0.011 0.001 TYR C 53 ARG 0.005 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 2.254 Fit side-chains REVERT: A 231 LEU cc_start: 0.8773 (tt) cc_final: 0.8522 (tm) REVERT: F 44 MET cc_start: 0.8837 (mtm) cc_final: 0.8579 (mtm) REVERT: I 4 MET cc_start: 0.7517 (mmt) cc_final: 0.7237 (mmt) REVERT: J 34 MET cc_start: 0.7102 (tpp) cc_final: 0.6785 (tpp) REVERT: K 376 MET cc_start: 0.9142 (ttp) cc_final: 0.8585 (ttm) REVERT: N 4 MET cc_start: 0.7658 (mmt) cc_final: 0.7356 (mmp) REVERT: O 18 MET cc_start: 0.7574 (ppp) cc_final: 0.7140 (pmm) REVERT: O 34 MET cc_start: 0.7229 (tpp) cc_final: 0.6993 (tpp) REVERT: O 94 TYR cc_start: 0.7574 (m-10) cc_final: 0.7140 (m-10) outliers start: 23 outliers final: 14 residues processed: 260 average time/residue: 1.0036 time to fit residues: 302.5732 Evaluate side-chains 254 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 150 HIS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 140 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN I 38 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN N 38 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18861 Z= 0.289 Angle : 0.591 8.984 25566 Z= 0.298 Chirality : 0.044 0.164 2784 Planarity : 0.005 0.042 3264 Dihedral : 4.865 26.263 2565 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.68 % Allowed : 12.13 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.52 (0.17), residues: 2325 helix: 0.02 (0.40), residues: 159 sheet: -0.02 (0.19), residues: 687 loop : -0.51 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 109 HIS 0.021 0.001 HIS F 150 PHE 0.011 0.002 PHE M 83 TYR 0.013 0.002 TYR B 80 ARG 0.003 0.000 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 2.107 Fit side-chains REVERT: F 44 MET cc_start: 0.8908 (mtm) cc_final: 0.8529 (mtm) REVERT: G 77 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: I 4 MET cc_start: 0.7559 (mmt) cc_final: 0.7198 (mmt) REVERT: J 34 MET cc_start: 0.7197 (tpp) cc_final: 0.6911 (tpp) REVERT: K 376 MET cc_start: 0.9081 (ttp) cc_final: 0.8783 (ttp) REVERT: L 87 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7161 (ptp-170) REVERT: M 53 ASN cc_start: 0.8628 (m110) cc_final: 0.8221 (m-40) REVERT: N 4 MET cc_start: 0.7665 (mmt) cc_final: 0.7335 (mmt) REVERT: O 94 TYR cc_start: 0.7595 (m-10) cc_final: 0.7108 (m-10) outliers start: 34 outliers final: 19 residues processed: 258 average time/residue: 1.0427 time to fit residues: 310.6523 Evaluate side-chains 262 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN H 37 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18861 Z= 0.286 Angle : 0.584 9.019 25566 Z= 0.294 Chirality : 0.044 0.157 2784 Planarity : 0.004 0.043 3264 Dihedral : 4.875 26.217 2565 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.82 % Allowed : 13.51 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.60 (0.17), residues: 2325 helix: 0.02 (0.40), residues: 159 sheet: -0.18 (0.18), residues: 747 loop : -0.52 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 109 HIS 0.004 0.001 HIS L 35 PHE 0.011 0.002 PHE K 311 TYR 0.011 0.001 TYR M 32 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 1.943 Fit side-chains REVERT: C 11 MET cc_start: 0.5559 (mmp) cc_final: 0.5179 (mmt) REVERT: F 44 MET cc_start: 0.8861 (mtm) cc_final: 0.8562 (mtm) REVERT: F 263 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.4914 (m-10) REVERT: G 77 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: I 4 MET cc_start: 0.7536 (mmt) cc_final: 0.7218 (mmt) REVERT: J 34 MET cc_start: 0.7281 (tpp) cc_final: 0.7000 (tpp) REVERT: K 263 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.5232 (m-10) REVERT: K 376 MET cc_start: 0.9069 (ttp) cc_final: 0.8755 (ttp) REVERT: N 4 MET cc_start: 0.7612 (mmt) cc_final: 0.7267 (mmp) REVERT: N 11 MET cc_start: 0.5269 (mmp) cc_final: 0.4969 (mmt) REVERT: O 18 MET cc_start: 0.7201 (pp-130) cc_final: 0.6655 (pmm) REVERT: O 94 TYR cc_start: 0.7612 (m-10) cc_final: 0.7159 (m-10) outliers start: 37 outliers final: 21 residues processed: 255 average time/residue: 0.9875 time to fit residues: 292.9767 Evaluate side-chains 258 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN C 89 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN M 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18861 Z= 0.258 Angle : 0.570 8.897 25566 Z= 0.287 Chirality : 0.043 0.154 2784 Planarity : 0.004 0.044 3264 Dihedral : 4.840 25.941 2565 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.22 % Allowed : 13.86 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.62 (0.17), residues: 2325 helix: 0.14 (0.41), residues: 159 sheet: -0.24 (0.18), residues: 747 loop : -0.51 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 109 HIS 0.011 0.001 HIS F 150 PHE 0.010 0.001 PHE M 83 TYR 0.010 0.001 TYR C 53 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.5395 (mmp) cc_final: 0.4974 (mmt) REVERT: F 44 MET cc_start: 0.8776 (mtm) cc_final: 0.8518 (mtm) REVERT: F 263 PHE cc_start: 0.5386 (OUTLIER) cc_final: 0.5027 (m-10) REVERT: G 77 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: H 93 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7673 (m-40) REVERT: J 34 MET cc_start: 0.7329 (tpp) cc_final: 0.6910 (tpp) REVERT: K 263 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.4979 (m-10) REVERT: K 376 MET cc_start: 0.9091 (ttp) cc_final: 0.8766 (ttp) REVERT: N 4 MET cc_start: 0.7604 (mmt) cc_final: 0.7259 (mmp) REVERT: O 18 MET cc_start: 0.7125 (pp-130) cc_final: 0.6397 (pmm) REVERT: O 94 TYR cc_start: 0.7684 (m-10) cc_final: 0.7346 (m-10) outliers start: 45 outliers final: 27 residues processed: 255 average time/residue: 1.0054 time to fit residues: 297.5365 Evaluate side-chains 265 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN I 90 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18861 Z= 0.241 Angle : 0.562 8.734 25566 Z= 0.283 Chirality : 0.043 0.152 2784 Planarity : 0.004 0.044 3264 Dihedral : 4.799 25.539 2565 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.12 % Allowed : 14.55 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.62 (0.17), residues: 2325 helix: 0.16 (0.42), residues: 159 sheet: -0.25 (0.18), residues: 744 loop : -0.52 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 109 HIS 0.004 0.001 HIS L 35 PHE 0.009 0.001 PHE M 83 TYR 0.010 0.001 TYR D 105 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7452 (tttp) REVERT: F 263 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.5011 (m-10) REVERT: G 77 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: H 93 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7649 (m-40) REVERT: I 4 MET cc_start: 0.7421 (mmt) cc_final: 0.7176 (mmt) REVERT: J 34 MET cc_start: 0.7357 (tpp) cc_final: 0.7014 (tpp) REVERT: K 263 PHE cc_start: 0.5417 (OUTLIER) cc_final: 0.5026 (m-10) REVERT: K 376 MET cc_start: 0.9087 (ttp) cc_final: 0.8760 (ttp) REVERT: L 87 ARG cc_start: 0.7733 (ptp-170) cc_final: 0.7426 (ptp-170) REVERT: N 4 MET cc_start: 0.7624 (mmt) cc_final: 0.7262 (mmp) REVERT: N 11 MET cc_start: 0.5528 (mmp) cc_final: 0.5292 (mmt) REVERT: O 18 MET cc_start: 0.7113 (pp-130) cc_final: 0.6464 (pmm) REVERT: O 94 TYR cc_start: 0.7672 (m-10) cc_final: 0.7223 (m-10) outliers start: 43 outliers final: 28 residues processed: 254 average time/residue: 0.9576 time to fit residues: 282.5106 Evaluate side-chains 265 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN I 90 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18861 Z= 0.254 Angle : 0.571 9.241 25566 Z= 0.287 Chirality : 0.043 0.153 2784 Planarity : 0.004 0.044 3264 Dihedral : 4.807 25.712 2565 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.42 % Allowed : 14.64 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.64 (0.17), residues: 2325 helix: 0.15 (0.42), residues: 159 sheet: -0.27 (0.18), residues: 744 loop : -0.53 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 109 HIS 0.012 0.001 HIS F 150 PHE 0.010 0.001 PHE G 95 TYR 0.010 0.001 TYR D 80 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4954 (mt) REVERT: D 65 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7462 (tttp) REVERT: E 107 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7027 (pmtt) REVERT: C 11 MET cc_start: 0.5557 (mmp) cc_final: 0.5174 (mmt) REVERT: F 263 PHE cc_start: 0.5342 (OUTLIER) cc_final: 0.5023 (m-10) REVERT: G 77 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (m-40) REVERT: H 93 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7652 (m-40) REVERT: J 34 MET cc_start: 0.7424 (tpp) cc_final: 0.7062 (tpp) REVERT: K 263 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.5156 (m-10) REVERT: K 376 MET cc_start: 0.9045 (ttp) cc_final: 0.8710 (ttp) REVERT: N 4 MET cc_start: 0.7628 (mmt) cc_final: 0.7260 (mmp) REVERT: O 18 MET cc_start: 0.7103 (pp-130) cc_final: 0.6478 (pmm) REVERT: O 94 TYR cc_start: 0.7669 (m-10) cc_final: 0.7324 (m-10) outliers start: 49 outliers final: 33 residues processed: 257 average time/residue: 0.9902 time to fit residues: 295.9161 Evaluate side-chains 270 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 150 HIS Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 172 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18861 Z= 0.343 Angle : 0.604 8.844 25566 Z= 0.305 Chirality : 0.045 0.188 2784 Planarity : 0.005 0.043 3264 Dihedral : 4.957 26.597 2565 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.51 % Allowed : 14.84 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.74 (0.17), residues: 2325 helix: 0.04 (0.42), residues: 159 sheet: -0.32 (0.18), residues: 744 loop : -0.60 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 109 HIS 0.029 0.002 HIS F 150 PHE 0.013 0.002 PHE J 45 TYR 0.014 0.002 TYR O 27 ARG 0.004 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4967 (mt) REVERT: D 65 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7511 (tttp) REVERT: E 107 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7037 (pmtt) REVERT: C 11 MET cc_start: 0.5576 (mmp) cc_final: 0.5200 (mmt) REVERT: F 263 PHE cc_start: 0.5413 (OUTLIER) cc_final: 0.5025 (m-10) REVERT: G 77 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: J 34 MET cc_start: 0.7372 (tpp) cc_final: 0.7022 (tpp) REVERT: K 263 PHE cc_start: 0.5416 (OUTLIER) cc_final: 0.5020 (m-10) REVERT: K 376 MET cc_start: 0.9036 (ttp) cc_final: 0.8712 (ttp) REVERT: L 87 ARG cc_start: 0.7773 (ptp-170) cc_final: 0.7520 (ptp-170) REVERT: N 4 MET cc_start: 0.7652 (mmt) cc_final: 0.7276 (mmp) REVERT: O 94 TYR cc_start: 0.7674 (m-10) cc_final: 0.7285 (m-10) outliers start: 51 outliers final: 35 residues processed: 269 average time/residue: 1.0112 time to fit residues: 314.7665 Evaluate side-chains 281 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18861 Z= 0.198 Angle : 0.552 9.821 25566 Z= 0.278 Chirality : 0.042 0.150 2784 Planarity : 0.004 0.045 3264 Dihedral : 4.748 24.848 2565 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.22 % Allowed : 15.14 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.65 (0.17), residues: 2325 helix: 0.21 (0.42), residues: 159 sheet: -0.27 (0.18), residues: 735 loop : -0.54 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 109 HIS 0.012 0.001 HIS F 150 PHE 0.009 0.001 PHE E 83 TYR 0.010 0.001 TYR D 105 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4964 (mt) REVERT: D 65 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7428 (tttp) REVERT: E 107 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6909 (pmtt) REVERT: C 4 MET cc_start: 0.7380 (mmt) cc_final: 0.6986 (tpp) REVERT: C 11 MET cc_start: 0.5526 (mmp) cc_final: 0.5144 (mmt) REVERT: F 263 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4955 (m-10) REVERT: J 34 MET cc_start: 0.7369 (tpp) cc_final: 0.7031 (tpp) REVERT: K 263 PHE cc_start: 0.5202 (OUTLIER) cc_final: 0.4863 (m-10) REVERT: K 376 MET cc_start: 0.9077 (ttp) cc_final: 0.8851 (ttp) REVERT: N 4 MET cc_start: 0.7600 (mmt) cc_final: 0.7304 (mmt) REVERT: N 11 MET cc_start: 0.5330 (mmp) cc_final: 0.5072 (mmt) REVERT: O 18 MET cc_start: 0.7374 (pp-130) cc_final: 0.6661 (pmm) REVERT: O 94 TYR cc_start: 0.7661 (m-10) cc_final: 0.7332 (m-10) outliers start: 45 outliers final: 30 residues processed: 265 average time/residue: 0.9728 time to fit residues: 300.5128 Evaluate side-chains 266 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 150 HIS Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 227 optimal weight: 0.5980 chunk 209 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 37 GLN C 89 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18861 Z= 0.257 Angle : 0.587 10.037 25566 Z= 0.293 Chirality : 0.043 0.153 2784 Planarity : 0.004 0.045 3264 Dihedral : 4.814 25.206 2565 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.07 % Allowed : 15.38 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.68 (0.17), residues: 2325 helix: 0.22 (0.42), residues: 159 sheet: -0.28 (0.18), residues: 735 loop : -0.58 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 109 HIS 0.014 0.001 HIS F 150 PHE 0.010 0.001 PHE G 95 TYR 0.017 0.001 TYR O 27 ARG 0.004 0.000 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4951 (mt) REVERT: A 385 MET cc_start: 0.6872 (tpp) cc_final: 0.6651 (tpt) REVERT: D 65 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7454 (tttp) REVERT: E 107 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6902 (pmtt) REVERT: C 11 MET cc_start: 0.5533 (mmp) cc_final: 0.5157 (mmt) REVERT: F 263 PHE cc_start: 0.5218 (OUTLIER) cc_final: 0.4836 (m-10) REVERT: G 77 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: H 107 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6773 (pmtt) REVERT: I 4 MET cc_start: 0.7598 (tpp) cc_final: 0.7203 (mmt) REVERT: J 34 MET cc_start: 0.7456 (tpp) cc_final: 0.7093 (tpp) REVERT: K 263 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4896 (m-10) REVERT: K 376 MET cc_start: 0.9039 (ttp) cc_final: 0.8715 (ttp) REVERT: L 87 ARG cc_start: 0.7744 (ptp-170) cc_final: 0.7459 (ptp-170) REVERT: N 4 MET cc_start: 0.7617 (mmt) cc_final: 0.7270 (mmp) REVERT: N 11 MET cc_start: 0.5355 (mmp) cc_final: 0.5079 (mmt) REVERT: O 18 MET cc_start: 0.7328 (pp-130) cc_final: 0.6522 (pmm) REVERT: O 94 TYR cc_start: 0.7726 (m-10) cc_final: 0.7277 (m-10) outliers start: 42 outliers final: 30 residues processed: 258 average time/residue: 0.9967 time to fit residues: 297.4674 Evaluate side-chains 269 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 181 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 159 optimal weight: 8.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.188392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122029 restraints weight = 41039.423| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.16 r_work: 0.3125 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18861 Z= 0.182 Angle : 0.551 10.324 25566 Z= 0.274 Chirality : 0.042 0.148 2784 Planarity : 0.004 0.049 3264 Dihedral : 4.640 23.536 2565 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.63 % Allowed : 15.88 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.58 (0.17), residues: 2325 helix: 0.38 (0.42), residues: 159 sheet: -0.21 (0.18), residues: 735 loop : -0.52 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 35 HIS 0.009 0.001 HIS F 150 PHE 0.008 0.001 PHE M 83 TYR 0.011 0.001 TYR D 105 ARG 0.003 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.55 seconds wall clock time: 110 minutes 42.41 seconds (6642.41 seconds total)