Starting phenix.real_space_refine on Sat Feb 17 15:11:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6j_27920/02_2024/8e6j_27920.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6j_27920/02_2024/8e6j_27920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6j_27920/02_2024/8e6j_27920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6j_27920/02_2024/8e6j_27920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6j_27920/02_2024/8e6j_27920.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6j_27920/02_2024/8e6j_27920.pdb" } resolution = 2.7 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 11944 2.51 5 N 3224 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19008 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "C" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "J" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "D" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Time building chain proxies: 10.42, per 1000 atoms: 0.55 Number of scatterers: 19008 At special positions: 0 Unit cell: (151.525, 151.525, 87, 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 112 16.00 O 3728 8.00 N 3224 7.00 C 11944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 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: 7.68 Conformation dependent library (CDL) restraints added in 3.7 seconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 48 sheets defined 3.4% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA A 203 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 205 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR A 252 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU A 267 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 254 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 256 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS A 280 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 363 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 372 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL H 96 " --> pdb=" O LEU H 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU H 100H" --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA B 203 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 205 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR B 252 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 267 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 254 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 256 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 280 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 363 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER B 372 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP E 35A" --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL E 96 " --> pdb=" O LEU E 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU E 100H" --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA C 203 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C 214 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 205 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR C 252 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 267 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 254 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 256 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS C 280 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 363 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 372 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 399 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR J 13 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR J 13 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'F' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP F 35A" --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL F 96 " --> pdb=" O LEU F 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU F 100H" --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA D 203 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D 214 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 205 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR D 252 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU D 267 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 254 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS D 256 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS D 280 " --> pdb=" O MET D 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 363 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 372 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA D 399 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR K 13 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR K 13 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP G 35A" --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL G 96 " --> pdb=" O LEU G 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU G 100H" --> pdb=" O VAL G 96 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1776 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: 7.62 Time building geometry restraints manager: 8.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6028 1.34 - 1.47: 5264 1.47 - 1.59: 8072 1.59 - 1.72: 0 1.72 - 1.84: 140 Bond restraints: 19504 Sorted by residual: bond pdb=" N CYS B 318 " pdb=" CA CYS B 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N CYS C 318 " pdb=" CA CYS C 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N CYS A 318 " pdb=" CA CYS A 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N CYS D 318 " pdb=" CA CYS D 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N LYS I 42 " pdb=" CA LYS I 42 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.59e+00 ... (remaining 19499 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.87: 852 106.87 - 113.68: 10084 113.68 - 120.48: 7612 120.48 - 127.29: 7636 127.29 - 134.09: 348 Bond angle restraints: 26532 Sorted by residual: angle pdb=" N CYS B 336 " pdb=" CA CYS B 336 " pdb=" C CYS B 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N CYS A 336 " pdb=" CA CYS A 336 " pdb=" C CYS A 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N CYS C 336 " pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N CYS D 336 " pdb=" CA CYS D 336 " pdb=" C CYS D 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N SER C 442 " pdb=" CA SER C 442 " pdb=" C SER C 442 " ideal model delta sigma weight residual 109.14 102.33 6.81 1.49e+00 4.50e-01 2.09e+01 ... (remaining 26527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 10756 17.54 - 35.08: 484 35.08 - 52.63: 152 52.63 - 70.17: 48 70.17 - 87.71: 20 Dihedral angle restraints: 11460 sinusoidal: 4444 harmonic: 7016 Sorted by residual: dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS A 183 " pdb=" SG CYS A 183 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 ... (remaining 11457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1732 0.049 - 0.097: 772 0.097 - 0.146: 268 0.146 - 0.195: 64 0.195 - 0.243: 24 Chirality restraints: 2860 Sorted by residual: chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE B 222 " pdb=" CA ILE B 222 " pdb=" CG1 ILE B 222 " pdb=" CG2 ILE B 222 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE C 222 " pdb=" CA ILE C 222 " pdb=" CG1 ILE C 222 " pdb=" CG2 ILE C 222 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2857 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 222 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE D 222 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE D 222 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU D 223 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 222 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE C 222 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 222 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU C 223 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 222 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE A 222 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE A 222 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 223 " 0.023 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 692 2.69 - 3.24: 17468 3.24 - 3.79: 31924 3.79 - 4.35: 45276 4.35 - 4.90: 74768 Nonbonded interactions: 170128 Sorted by model distance: nonbonded pdb=" O ASP A 113 " pdb=" OG SER A 168 " model vdw 2.136 2.440 nonbonded pdb=" O ASP C 113 " pdb=" OG SER C 168 " model vdw 2.136 2.440 nonbonded pdb=" O ASP D 113 " pdb=" OG SER D 168 " model vdw 2.136 2.440 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 168 " model vdw 2.136 2.440 nonbonded pdb=" OG SER A 298 " pdb=" O SER A 343 " model vdw 2.230 2.440 ... (remaining 170123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.390 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 54.890 Find NCS groups from input model: 1.290 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: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.007 0.089 19504 Z= 0.439 Angle : 1.171 7.083 26532 Z= 0.686 Chirality : 0.064 0.243 2860 Planarity : 0.006 0.039 3408 Dihedral : 12.050 87.709 6884 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.47 (0.17), residues: 2444 helix: 0.36 (0.79), residues: 24 sheet: 0.71 (0.17), residues: 884 loop : 0.15 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP I 35 HIS 0.012 0.003 HIS D 412A PHE 0.022 0.004 PHE B 446 TYR 0.043 0.004 TYR E 34 ARG 0.009 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 2.447 Fit side-chains REVERT: A 358 ASN cc_start: 0.7852 (m110) cc_final: 0.7544 (t0) REVERT: H 100 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7630 (mmt90) REVERT: B 358 ASN cc_start: 0.7853 (m110) cc_final: 0.7544 (t0) REVERT: E 100 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7631 (mmt90) REVERT: C 358 ASN cc_start: 0.7852 (m110) cc_final: 0.7541 (t0) REVERT: F 100 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7632 (mmt90) REVERT: D 358 ASN cc_start: 0.7849 (m110) cc_final: 0.7538 (t0) REVERT: G 100 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7631 (mmt90) outliers start: 4 outliers final: 0 residues processed: 248 average time/residue: 0.8935 time to fit residues: 262.9029 Evaluate side-chains 192 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 274 HIS A 347 ASN A 450 ASN H 81 ASN B 226 GLN B 274 HIS B 347 ASN B 450 ASN E 81 ASN C 226 GLN C 274 HIS C 347 ASN C 450 ASN F 81 ASN D 226 GLN D 274 HIS D 347 ASN D 450 ASN G 81 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19504 Z= 0.276 Angle : 0.620 9.703 26532 Z= 0.341 Chirality : 0.049 0.155 2860 Planarity : 0.004 0.032 3408 Dihedral : 5.342 20.597 2664 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.43 % Allowed : 8.61 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.50 (0.17), residues: 2444 helix: -0.07 (0.76), residues: 28 sheet: 0.61 (0.16), residues: 992 loop : 0.24 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 47 HIS 0.008 0.002 HIS D 412A PHE 0.018 0.002 PHE A 410 TYR 0.015 0.002 TYR A 169A ARG 0.003 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 2.189 Fit side-chains REVERT: A 172 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7405 (ttm170) REVERT: A 358 ASN cc_start: 0.7855 (m110) cc_final: 0.7556 (t0) REVERT: L 37 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: B 172 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7404 (ttm170) REVERT: B 358 ASN cc_start: 0.7856 (m110) cc_final: 0.7559 (t0) REVERT: I 37 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: C 172 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7406 (ttm170) REVERT: C 358 ASN cc_start: 0.7854 (m110) cc_final: 0.7555 (t0) REVERT: J 37 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: D 172 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7406 (ttm170) REVERT: D 358 ASN cc_start: 0.7853 (m110) cc_final: 0.7555 (t0) REVERT: K 37 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7648 (tt0) outliers start: 52 outliers final: 16 residues processed: 236 average time/residue: 1.1275 time to fit residues: 305.7834 Evaluate side-chains 220 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 37 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN A 347 ASN L 89 GLN B 226 GLN B 294 ASN B 347 ASN I 89 GLN C 226 GLN C 294 ASN C 347 ASN J 89 GLN D 226 GLN D 294 ASN D 347 ASN K 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19504 Z= 0.339 Angle : 0.641 8.178 26532 Z= 0.348 Chirality : 0.050 0.250 2860 Planarity : 0.004 0.042 3408 Dihedral : 5.633 42.086 2664 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 2.25 % Allowed : 9.55 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.31 (0.17), residues: 2444 helix: -0.94 (0.79), residues: 28 sheet: 0.42 (0.16), residues: 988 loop : 0.19 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.009 0.003 HIS C 296 PHE 0.020 0.003 PHE C 121 TYR 0.012 0.002 TYR D 169A ARG 0.003 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.210 Fit side-chains REVERT: A 358 ASN cc_start: 0.7883 (m110) cc_final: 0.7536 (t0) REVERT: L 37 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: B 358 ASN cc_start: 0.7881 (m110) cc_final: 0.7536 (t0) REVERT: I 37 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: C 358 ASN cc_start: 0.7881 (m110) cc_final: 0.7535 (t0) REVERT: J 37 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: D 358 ASN cc_start: 0.7880 (m110) cc_final: 0.7535 (t0) REVERT: K 37 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7694 (tt0) outliers start: 48 outliers final: 32 residues processed: 220 average time/residue: 1.1265 time to fit residues: 285.8496 Evaluate side-chains 220 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN A 296 HIS L 89 GLN H 81 ASN B 226 GLN B 294 ASN B 296 HIS I 89 GLN E 81 ASN C 226 GLN C 294 ASN C 296 HIS J 89 GLN F 81 ASN D 226 GLN D 294 ASN D 296 HIS K 89 GLN G 81 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19504 Z= 0.221 Angle : 0.553 7.473 26532 Z= 0.299 Chirality : 0.046 0.164 2860 Planarity : 0.004 0.040 3408 Dihedral : 5.333 37.542 2664 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.22 % Rotamer: Outliers : 2.25 % Allowed : 10.86 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.33 (0.17), residues: 2444 helix: -1.02 (0.73), residues: 28 sheet: 0.45 (0.16), residues: 976 loop : 0.19 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.004 0.001 HIS G 95 PHE 0.016 0.002 PHE A 121 TYR 0.010 0.002 TYR K 49 ARG 0.002 0.000 ARG D 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.383 Fit side-chains REVERT: A 358 ASN cc_start: 0.7870 (m110) cc_final: 0.7538 (t0) REVERT: B 358 ASN cc_start: 0.7869 (m110) cc_final: 0.7538 (t0) REVERT: C 358 ASN cc_start: 0.7871 (m110) cc_final: 0.7539 (t0) REVERT: D 358 ASN cc_start: 0.7868 (m110) cc_final: 0.7537 (t0) outliers start: 48 outliers final: 28 residues processed: 228 average time/residue: 1.1232 time to fit residues: 294.2460 Evaluate side-chains 216 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN A 296 HIS L 89 GLN B 226 GLN B 294 ASN B 296 HIS I 89 GLN C 226 GLN C 294 ASN C 296 HIS J 89 GLN D 226 GLN D 294 ASN D 296 HIS K 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 19504 Z= 0.472 Angle : 0.674 9.036 26532 Z= 0.366 Chirality : 0.052 0.184 2860 Planarity : 0.005 0.048 3408 Dihedral : 5.906 37.907 2664 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Rotamer: Outliers : 3.93 % Allowed : 10.67 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.10 (0.17), residues: 2444 helix: -1.17 (0.84), residues: 24 sheet: 0.33 (0.15), residues: 1000 loop : -0.01 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 97 HIS 0.007 0.002 HIS G 95 PHE 0.027 0.003 PHE C 121 TYR 0.014 0.002 TYR E 100G ARG 0.004 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 180 time to evaluate : 2.444 Fit side-chains outliers start: 84 outliers final: 44 residues processed: 248 average time/residue: 1.0908 time to fit residues: 315.4142 Evaluate side-chains 228 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 0.0020 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 226 GLN A 296 HIS L 89 GLN H 76 ASN H 81 ASN B 170 ASN B 226 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN E 76 ASN E 81 ASN C 170 ASN C 226 GLN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN F 76 ASN F 81 ASN D 170 ASN D 226 GLN D 296 HIS K 89 GLN G 76 ASN G 81 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19504 Z= 0.208 Angle : 0.541 7.437 26532 Z= 0.293 Chirality : 0.047 0.200 2860 Planarity : 0.004 0.040 3408 Dihedral : 5.337 41.121 2664 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 2.15 % Allowed : 13.20 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.27 (0.17), residues: 2444 helix: -0.85 (0.78), residues: 24 sheet: 0.44 (0.16), residues: 996 loop : 0.11 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 178 HIS 0.003 0.001 HIS G 95 PHE 0.019 0.002 PHE B 410 TYR 0.010 0.001 TYR K 49 ARG 0.003 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 2.288 Fit side-chains REVERT: A 358 ASN cc_start: 0.7981 (m110) cc_final: 0.7461 (t0) REVERT: B 358 ASN cc_start: 0.7978 (m110) cc_final: 0.7460 (t0) REVERT: C 358 ASN cc_start: 0.7979 (m110) cc_final: 0.7461 (t0) REVERT: D 358 ASN cc_start: 0.7978 (m110) cc_final: 0.7460 (t0) outliers start: 46 outliers final: 16 residues processed: 218 average time/residue: 1.1197 time to fit residues: 279.9475 Evaluate side-chains 204 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 0.0970 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS L 89 GLN H 76 ASN B 226 GLN B 296 HIS I 89 GLN E 76 ASN C 226 GLN C 296 HIS J 89 GLN F 76 ASN D 226 GLN D 296 HIS K 89 GLN G 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19504 Z= 0.215 Angle : 0.534 7.673 26532 Z= 0.289 Chirality : 0.046 0.174 2860 Planarity : 0.004 0.039 3408 Dihedral : 5.239 39.039 2664 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 2.81 % Allowed : 12.55 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.31 (0.17), residues: 2444 helix: -1.12 (0.71), residues: 28 sheet: 0.50 (0.16), residues: 992 loop : 0.12 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 178 HIS 0.003 0.001 HIS G 95 PHE 0.019 0.002 PHE C 121 TYR 0.012 0.001 TYR I 49 ARG 0.002 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 184 time to evaluate : 2.287 Fit side-chains REVERT: A 358 ASN cc_start: 0.8066 (m110) cc_final: 0.7504 (t0) REVERT: A 396 ASP cc_start: 0.8568 (m-30) cc_final: 0.8355 (m-30) REVERT: B 358 ASN cc_start: 0.8064 (m110) cc_final: 0.7503 (t0) REVERT: B 396 ASP cc_start: 0.8569 (m-30) cc_final: 0.8358 (m-30) REVERT: C 358 ASN cc_start: 0.8066 (m110) cc_final: 0.7505 (t0) REVERT: C 396 ASP cc_start: 0.8570 (m-30) cc_final: 0.8356 (m-30) REVERT: D 358 ASN cc_start: 0.8064 (m110) cc_final: 0.7504 (t0) REVERT: D 396 ASP cc_start: 0.8570 (m-30) cc_final: 0.8357 (m-30) outliers start: 60 outliers final: 28 residues processed: 228 average time/residue: 1.1143 time to fit residues: 293.0866 Evaluate side-chains 212 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS L 89 GLN H 81 ASN B 226 GLN B 296 HIS I 89 GLN E 81 ASN C 226 GLN C 296 HIS J 89 GLN F 81 ASN D 226 GLN D 296 HIS K 89 GLN G 76 ASN G 81 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19504 Z= 0.222 Angle : 0.534 7.438 26532 Z= 0.289 Chirality : 0.046 0.167 2860 Planarity : 0.004 0.038 3408 Dihedral : 5.201 37.555 2664 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 13.44 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.31 (0.17), residues: 2444 helix: -1.09 (0.72), residues: 28 sheet: 0.49 (0.16), residues: 992 loop : 0.12 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.003 0.001 HIS G 95 PHE 0.019 0.002 PHE A 121 TYR 0.011 0.001 TYR I 49 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 2.066 Fit side-chains REVERT: A 358 ASN cc_start: 0.8052 (m110) cc_final: 0.7509 (t0) REVERT: A 396 ASP cc_start: 0.8568 (m-30) cc_final: 0.8353 (m-30) REVERT: A 430 GLN cc_start: 0.8338 (mm110) cc_final: 0.8042 (mt0) REVERT: B 358 ASN cc_start: 0.8049 (m110) cc_final: 0.7507 (t0) REVERT: B 396 ASP cc_start: 0.8569 (m-30) cc_final: 0.8355 (m-30) REVERT: B 430 GLN cc_start: 0.8341 (mm110) cc_final: 0.8042 (mt0) REVERT: C 358 ASN cc_start: 0.8051 (m110) cc_final: 0.7508 (t0) REVERT: C 396 ASP cc_start: 0.8568 (m-30) cc_final: 0.8354 (m-30) REVERT: C 430 GLN cc_start: 0.8340 (mm110) cc_final: 0.8043 (mt0) REVERT: D 358 ASN cc_start: 0.8050 (m110) cc_final: 0.7509 (t0) REVERT: D 396 ASP cc_start: 0.8569 (m-30) cc_final: 0.8355 (m-30) REVERT: D 430 GLN cc_start: 0.8341 (mm110) cc_final: 0.8044 (mt0) outliers start: 53 outliers final: 37 residues processed: 229 average time/residue: 1.1412 time to fit residues: 300.6598 Evaluate side-chains 221 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS L 89 GLN H 81 ASN B 226 GLN B 296 HIS I 89 GLN E 81 ASN C 226 GLN C 296 HIS J 89 GLN F 81 ASN D 226 GLN D 296 HIS K 89 GLN G 81 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19504 Z= 0.395 Angle : 0.632 8.948 26532 Z= 0.342 Chirality : 0.050 0.199 2860 Planarity : 0.005 0.046 3408 Dihedral : 5.634 39.318 2664 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 2.72 % Allowed : 13.95 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.19 (0.17), residues: 2444 helix: -1.05 (0.85), residues: 24 sheet: 0.42 (0.16), residues: 992 loop : 0.02 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 97 HIS 0.006 0.002 HIS E 95 PHE 0.026 0.003 PHE A 121 TYR 0.013 0.002 TYR E 100G ARG 0.002 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 164 time to evaluate : 2.422 Fit side-chains REVERT: A 358 ASN cc_start: 0.8081 (m110) cc_final: 0.7520 (t0) REVERT: A 430 GLN cc_start: 0.8359 (mm110) cc_final: 0.8123 (mt0) REVERT: B 358 ASN cc_start: 0.8079 (m110) cc_final: 0.7518 (t0) REVERT: B 430 GLN cc_start: 0.8359 (mm110) cc_final: 0.8123 (mt0) REVERT: C 358 ASN cc_start: 0.8079 (m110) cc_final: 0.7517 (t0) REVERT: C 430 GLN cc_start: 0.8361 (mm110) cc_final: 0.8125 (mt0) REVERT: D 358 ASN cc_start: 0.8080 (m110) cc_final: 0.7520 (t0) REVERT: D 430 GLN cc_start: 0.8360 (mm110) cc_final: 0.8124 (mt0) outliers start: 58 outliers final: 38 residues processed: 207 average time/residue: 1.0424 time to fit residues: 250.4297 Evaluate side-chains 202 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS L 89 GLN H 81 ASN B 226 GLN B 296 HIS I 89 GLN E 81 ASN C 226 GLN C 296 HIS J 89 GLN F 81 ASN D 226 GLN D 296 HIS K 89 GLN G 81 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19504 Z= 0.291 Angle : 0.582 8.204 26532 Z= 0.315 Chirality : 0.048 0.167 2860 Planarity : 0.004 0.043 3408 Dihedral : 5.464 38.521 2664 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 2.43 % Allowed : 14.42 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.21 (0.17), residues: 2444 helix: -0.96 (0.83), residues: 24 sheet: 0.45 (0.16), residues: 992 loop : 0.02 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 178 HIS 0.004 0.001 HIS G 95 PHE 0.022 0.002 PHE B 121 TYR 0.011 0.002 TYR I 49 ARG 0.002 0.000 ARG C 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 2.496 Fit side-chains REVERT: A 150 LYS cc_start: 0.8044 (pttm) cc_final: 0.7714 (pttp) REVERT: A 358 ASN cc_start: 0.8053 (m110) cc_final: 0.7503 (t0) REVERT: A 430 GLN cc_start: 0.8365 (mm110) cc_final: 0.8159 (mm110) REVERT: B 150 LYS cc_start: 0.8045 (pttm) cc_final: 0.7716 (pttp) REVERT: B 358 ASN cc_start: 0.8050 (m110) cc_final: 0.7501 (t0) REVERT: B 430 GLN cc_start: 0.8365 (mm110) cc_final: 0.8158 (mm110) REVERT: C 150 LYS cc_start: 0.8044 (pttm) cc_final: 0.7716 (pttp) REVERT: C 358 ASN cc_start: 0.8051 (m110) cc_final: 0.7501 (t0) REVERT: C 430 GLN cc_start: 0.8366 (mm110) cc_final: 0.8159 (mm110) REVERT: D 150 LYS cc_start: 0.8044 (pttm) cc_final: 0.7715 (pttp) REVERT: D 358 ASN cc_start: 0.8052 (m110) cc_final: 0.7501 (t0) REVERT: D 430 GLN cc_start: 0.8365 (mm110) cc_final: 0.8160 (mm110) outliers start: 52 outliers final: 40 residues processed: 208 average time/residue: 1.0766 time to fit residues: 258.7611 Evaluate side-chains 208 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS L 89 GLN H 81 ASN B 226 GLN B 296 HIS I 89 GLN E 81 ASN C 226 GLN C 296 HIS J 89 GLN F 81 ASN D 226 GLN D 296 HIS K 89 GLN G 81 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122543 restraints weight = 21840.379| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.41 r_work: 0.3263 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19504 Z= 0.266 Angle : 0.562 8.042 26532 Z= 0.303 Chirality : 0.047 0.163 2860 Planarity : 0.004 0.041 3408 Dihedral : 5.370 37.470 2664 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 2.67 % Allowed : 14.19 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.23 (0.17), residues: 2444 helix: -0.91 (0.80), residues: 24 sheet: 0.46 (0.16), residues: 992 loop : 0.04 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.004 0.001 HIS E 95 PHE 0.021 0.002 PHE B 121 TYR 0.012 0.002 TYR J 49 ARG 0.002 0.000 ARG D 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5881.15 seconds wall clock time: 107 minutes 22.40 seconds (6442.40 seconds total)