Starting phenix.real_space_refine on Sun Jun 30 02:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/06_2024/8v5k_42983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/06_2024/8v5k_42983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/06_2024/8v5k_42983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/06_2024/8v5k_42983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/06_2024/8v5k_42983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/06_2024/8v5k_42983.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4551 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 9654 2.51 5 N 2655 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 48": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "H ARG 20": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 48": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 43": "NH1" <-> "NH2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15336 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3256 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 14, 'TRANS': 404} Chain breaks: 5 Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "G" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3256 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 14, 'TRANS': 404} Chain breaks: 5 Chain: "C" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3256 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 14, 'TRANS': 404} Chain breaks: 5 Chain: "E" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "F" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.69, per 1000 atoms: 0.57 Number of scatterers: 15336 At special positions: 0 Unit cell: (134.42, 134.42, 125.96, 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 69 16.00 O 2958 8.00 N 2655 7.00 C 9654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.04 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.02 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.04 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 104 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 104 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 359 " " NAG B 601 " - " ASN B 359 " " NAG C 601 " - " ASN C 359 " Time building additional restraints: 5.58 Conformation dependent library (CDL) restraints added in 2.4 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 33 sheets defined 29.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 64 through 91 removed outlier: 4.155A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 125 through 154 removed outlier: 4.677A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 191 removed outlier: 4.062A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.998A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.553A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 481 Processing helix chain 'D' and resid 26 through 29 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.837A pdb=" N THR G 99 " --> pdb=" O PRO G 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 64 through 91 removed outlier: 4.167A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 125 through 154 removed outlier: 4.712A pdb=" N GLN B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.032A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.127A pdb=" N LEU B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.738A pdb=" N ILE B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.553A pdb=" N ILE B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 481 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 64 through 91 removed outlier: 4.163A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 125 through 137 Processing helix chain 'C' and resid 137 through 154 removed outlier: 3.628A pdb=" N SER C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 191 removed outlier: 4.014A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.982A pdb=" N LEU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.756A pdb=" N ILE C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 481 Processing helix chain 'E' and resid 27 through 30 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 112A through 113 No H-bonds generated for 'chain 'E' and resid 112A through 113' Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 112A through 113 No H-bonds generated for 'chain 'F' and resid 112A through 113' Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.851A pdb=" N THR H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 84 No H-bonds generated for 'chain 'I' and resid 82 through 84' Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.832A pdb=" N THR I 99 " --> pdb=" O PRO I 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.778A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS A 263 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG A 281 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 269 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE A 293 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY A 37 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR A 291 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.849A pdb=" N THR A 117 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL A 114 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN C 428 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 116 " --> pdb=" O ASN C 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 removed outlier: 6.854A pdb=" N LEU A 426 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 116 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR B 117 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.370A pdb=" N VAL D 12 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG D 40 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.370A pdb=" N VAL D 12 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS D 98 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TRP D 114 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL D 100 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 2 through 7 removed outlier: 3.605A pdb=" N THR G 77 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 13 removed outlier: 8.108A pdb=" N LYS G 37 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR G 57 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 39 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP G 41 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AB6, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.360A pdb=" N THR B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 269 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 293 " --> pdb=" O PRO B 35 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 37 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N THR B 291 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 394 removed outlier: 8.177A pdb=" N LEU B 426 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR C 117 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN B 428 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 117 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.400A pdb=" N THR C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 269 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN C 43 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR C 286 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C 41 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 293 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY C 37 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR C 291 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.336A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG E 43 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE E 52 " --> pdb=" O ARG E 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.336A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS E 104 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TRP E 118 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 106 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.339A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG F 43 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.339A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS F 104 " --> pdb=" O TRP F 118 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TRP F 118 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F 106 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 2 through 7 removed outlier: 3.566A pdb=" N THR H 77 " --> pdb=" O ARG H 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 13 removed outlier: 8.159A pdb=" N LYS H 37 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR H 57 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU H 39 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER H 55 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AD4, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.587A pdb=" N THR I 77 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 13 removed outlier: 8.073A pdb=" N LYS I 37 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR I 57 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU I 39 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 11 through 13 787 hydrogen bonds defined for protein. 2079 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: 5.41 Time building geometry restraints manager: 6.19 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: 5085 1.34 - 1.46: 2686 1.46 - 1.58: 7709 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 15570 Sorted by residual: bond pdb=" CB THR A 393 " pdb=" CG2 THR A 393 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.13e+00 bond pdb=" CB THR B 393 " pdb=" CG2 THR B 393 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CB THR C 393 " pdb=" CG2 THR C 393 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.12e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 15565 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.42: 333 106.42 - 113.33: 8613 113.33 - 120.23: 5470 120.23 - 127.14: 6542 127.14 - 134.04: 126 Bond angle restraints: 21084 Sorted by residual: angle pdb=" N SER C 174 " pdb=" CA SER C 174 " pdb=" C SER C 174 " ideal model delta sigma weight residual 111.02 115.74 -4.72 1.22e+00 6.72e-01 1.50e+01 angle pdb=" N SER B 174 " pdb=" CA SER B 174 " pdb=" C SER B 174 " ideal model delta sigma weight residual 111.02 115.59 -4.57 1.22e+00 6.72e-01 1.40e+01 angle pdb=" N SER A 174 " pdb=" CA SER A 174 " pdb=" C SER A 174 " ideal model delta sigma weight residual 111.02 115.55 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" CA LEU B 78 " pdb=" CB LEU B 78 " pdb=" CG LEU B 78 " ideal model delta sigma weight residual 116.30 126.84 -10.54 3.50e+00 8.16e-02 9.06e+00 angle pdb=" N CYS A 394 " pdb=" CA CYS A 394 " pdb=" C CYS A 394 " ideal model delta sigma weight residual 108.90 113.51 -4.61 1.63e+00 3.76e-01 8.01e+00 ... (remaining 21079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 8954 17.50 - 35.00: 449 35.00 - 52.49: 69 52.49 - 69.99: 21 69.99 - 87.49: 23 Dihedral angle restraints: 9516 sinusoidal: 3831 harmonic: 5685 Sorted by residual: dihedral pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -134.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -132.96 46.96 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -130.65 44.65 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 9513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1450 0.040 - 0.079: 677 0.079 - 0.119: 264 0.119 - 0.158: 57 0.158 - 0.198: 12 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA LEU G 114 " pdb=" N LEU G 114 " pdb=" C LEU G 114 " pdb=" CB LEU G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CG LEU G 4 " pdb=" CB LEU G 4 " pdb=" CD1 LEU G 4 " pdb=" CD2 LEU G 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA LEU I 114 " pdb=" N LEU I 114 " pdb=" C LEU I 114 " pdb=" CB LEU I 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2457 not shown) Planarity restraints: 2703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 281 " -0.316 9.50e-02 1.11e+02 1.45e-01 2.39e+01 pdb=" NE ARG B 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG B 281 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B 281 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 281 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 281 " 0.279 9.50e-02 1.11e+02 1.28e-01 1.77e+01 pdb=" NE ARG A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG A 281 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 281 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 281 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 281 " 0.226 9.50e-02 1.11e+02 1.04e-01 1.20e+01 pdb=" NE ARG C 281 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG C 281 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG C 281 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 281 " 0.022 2.00e-02 2.50e+03 ... (remaining 2700 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1756 2.75 - 3.29: 14538 3.29 - 3.83: 24006 3.83 - 4.36: 29604 4.36 - 4.90: 51468 Nonbonded interactions: 121372 Sorted by model distance: nonbonded pdb=" OG SER G 55 " pdb=" OD1 ASN G 66 " model vdw 2.217 2.440 nonbonded pdb=" OG SER H 55 " pdb=" OD1 ASN H 66 " model vdw 2.236 2.440 nonbonded pdb=" OG SER G 7 " pdb=" OG SER G 22 " model vdw 2.242 2.440 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.263 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 22 " model vdw 2.264 2.440 ... (remaining 121367 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 7.060 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 41.300 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 0.088 15570 Z= 0.444 Angle : 0.752 10.536 21084 Z= 0.423 Chirality : 0.052 0.198 2460 Planarity : 0.006 0.145 2700 Dihedral : 11.790 87.490 5796 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.72 (0.19), residues: 1932 helix: 0.07 (0.23), residues: 423 sheet: 0.62 (0.20), residues: 580 loop : 0.80 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 473 HIS 0.008 0.002 HIS D 30 PHE 0.027 0.003 PHE C 111 TYR 0.044 0.004 TYR I 117 ARG 0.059 0.002 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7555 (mm110) cc_final: 0.7303 (mm110) REVERT: A 136 GLU cc_start: 0.7401 (tt0) cc_final: 0.6986 (tt0) REVERT: A 181 LYS cc_start: 0.7978 (mttm) cc_final: 0.7622 (mttm) REVERT: A 193 GLU cc_start: 0.7194 (tt0) cc_final: 0.6939 (tt0) REVERT: A 261 SER cc_start: 0.8048 (t) cc_final: 0.7723 (p) REVERT: A 349 ASN cc_start: 0.7371 (t0) cc_final: 0.7024 (t0) REVERT: A 351 GLU cc_start: 0.7564 (mp0) cc_final: 0.6919 (mp0) REVERT: A 466 ASP cc_start: 0.7629 (m-30) cc_final: 0.7325 (m-30) REVERT: G 117 TYR cc_start: 0.8303 (m-10) cc_final: 0.7873 (m-80) REVERT: B 21 ASP cc_start: 0.7891 (t70) cc_final: 0.7622 (t0) REVERT: B 38 MET cc_start: 0.7640 (ttp) cc_final: 0.7433 (ttm) REVERT: B 66 GLN cc_start: 0.7439 (tp-100) cc_final: 0.7144 (tp-100) REVERT: B 189 ARG cc_start: 0.6508 (ttp-110) cc_final: 0.6186 (ttp-110) REVERT: B 287 ARG cc_start: 0.7196 (ttt-90) cc_final: 0.6931 (ttt-90) REVERT: B 362 GLN cc_start: 0.8466 (mm110) cc_final: 0.8085 (mm110) REVERT: B 406 ASP cc_start: 0.7891 (p0) cc_final: 0.7670 (p0) REVERT: B 462 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7439 (ttmm) REVERT: B 466 ASP cc_start: 0.7520 (m-30) cc_final: 0.7259 (m-30) REVERT: B 468 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7030 (mm-30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 1.4067 time to fit residues: 571.1491 Evaluate side-chains 312 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 174 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 42 GLN A 304 GLN B 418 ASN C 290 ASN C 304 GLN C 399 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15570 Z= 0.230 Angle : 0.600 9.350 21084 Z= 0.321 Chirality : 0.046 0.177 2460 Planarity : 0.004 0.035 2700 Dihedral : 5.131 32.035 2205 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.61 % Allowed : 8.53 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.29 (0.19), residues: 1932 helix: 1.14 (0.24), residues: 453 sheet: 0.93 (0.20), residues: 561 loop : 0.86 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 473 HIS 0.005 0.001 HIS D 30 PHE 0.013 0.002 PHE C 111 TYR 0.020 0.002 TYR I 117 ARG 0.008 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 321 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7436 (mm110) cc_final: 0.7200 (mm110) REVERT: A 136 GLU cc_start: 0.7381 (tt0) cc_final: 0.7104 (tt0) REVERT: A 189 ARG cc_start: 0.6411 (ttp-110) cc_final: 0.6123 (ttp-110) REVERT: A 193 GLU cc_start: 0.7201 (tt0) cc_final: 0.6952 (tt0) REVERT: A 351 GLU cc_start: 0.7549 (mp0) cc_final: 0.7149 (mp0) REVERT: A 466 ASP cc_start: 0.7566 (m-30) cc_final: 0.7340 (m-30) REVERT: B 70 GLN cc_start: 0.7480 (mm110) cc_final: 0.7265 (mm-40) REVERT: B 287 ARG cc_start: 0.7103 (ttt-90) cc_final: 0.6832 (ttt-90) REVERT: B 462 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7409 (ttmm) REVERT: B 466 ASP cc_start: 0.7502 (m-30) cc_final: 0.7218 (m-30) REVERT: B 468 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6927 (mm-30) outliers start: 44 outliers final: 16 residues processed: 335 average time/residue: 1.4538 time to fit residues: 528.2302 Evaluate side-chains 320 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 304 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN C 42 GLN C 290 ASN C 304 GLN C 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15570 Z= 0.284 Angle : 0.587 9.215 21084 Z= 0.307 Chirality : 0.045 0.150 2460 Planarity : 0.004 0.036 2700 Dihedral : 4.755 23.360 2205 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.90 % Allowed : 10.54 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.35 (0.19), residues: 1932 helix: 1.51 (0.25), residues: 453 sheet: 0.73 (0.20), residues: 582 loop : 0.88 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 473 HIS 0.004 0.001 HIS A 315 PHE 0.016 0.002 PHE C 346 TYR 0.017 0.002 TYR I 117 ARG 0.010 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 307 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6481 (ttp-110) cc_final: 0.6150 (ttp-110) REVERT: A 193 GLU cc_start: 0.7162 (tt0) cc_final: 0.6909 (tt0) REVERT: B 70 GLN cc_start: 0.7487 (mm110) cc_final: 0.7280 (mm-40) REVERT: B 287 ARG cc_start: 0.7120 (ttt-90) cc_final: 0.6851 (ttt-90) REVERT: B 462 LYS cc_start: 0.7764 (ttmm) cc_final: 0.7388 (ttmm) REVERT: B 466 ASP cc_start: 0.7526 (m-30) cc_final: 0.7225 (m-30) REVERT: B 468 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 466 ASP cc_start: 0.7520 (m-30) cc_final: 0.7272 (m-30) outliers start: 49 outliers final: 22 residues processed: 327 average time/residue: 1.4926 time to fit residues: 528.7951 Evaluate side-chains 321 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 299 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 0.0770 chunk 185 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15570 Z= 0.171 Angle : 0.531 8.549 21084 Z= 0.277 Chirality : 0.043 0.140 2460 Planarity : 0.004 0.041 2700 Dihedral : 4.434 21.528 2205 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.61 % Allowed : 12.02 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.40 (0.19), residues: 1932 helix: 1.77 (0.25), residues: 453 sheet: 0.78 (0.20), residues: 573 loop : 0.76 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 473 HIS 0.003 0.001 HIS F 31 PHE 0.012 0.001 PHE C 346 TYR 0.013 0.001 TYR A 294 ARG 0.011 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 307 time to evaluate : 1.738 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6507 (ttp-110) cc_final: 0.6179 (ttp-110) REVERT: A 193 GLU cc_start: 0.7101 (tt0) cc_final: 0.6867 (tt0) REVERT: A 255 ASP cc_start: 0.7377 (m-30) cc_final: 0.7156 (m-30) REVERT: B 189 ARG cc_start: 0.6495 (ttp-110) cc_final: 0.6237 (ttp-110) REVERT: B 287 ARG cc_start: 0.7098 (ttt-90) cc_final: 0.6831 (ttt-90) REVERT: B 462 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7341 (ttmm) REVERT: B 466 ASP cc_start: 0.7515 (m-30) cc_final: 0.7212 (m-30) REVERT: B 468 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6871 (mm-30) REVERT: C 351 GLU cc_start: 0.7723 (mp0) cc_final: 0.7105 (mp0) REVERT: C 466 ASP cc_start: 0.7509 (m-30) cc_final: 0.7263 (m-30) REVERT: C 468 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6833 (mm-30) REVERT: F 123 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7566 (tm-30) outliers start: 44 outliers final: 22 residues processed: 324 average time/residue: 1.3847 time to fit residues: 487.7729 Evaluate side-chains 319 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 296 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 70 GLN B 304 GLN B 447 ASN C 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15570 Z= 0.418 Angle : 0.622 10.609 21084 Z= 0.317 Chirality : 0.047 0.185 2460 Planarity : 0.004 0.039 2700 Dihedral : 4.603 20.947 2205 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.96 % Allowed : 13.03 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.17 (0.19), residues: 1932 helix: 1.68 (0.25), residues: 453 sheet: 0.51 (0.20), residues: 582 loop : 0.66 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 473 HIS 0.004 0.001 HIS D 30 PHE 0.021 0.002 PHE C 346 TYR 0.020 0.002 TYR B 294 ARG 0.009 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 314 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: A 189 ARG cc_start: 0.6551 (ttp-110) cc_final: 0.6203 (ttp-110) REVERT: A 193 GLU cc_start: 0.7141 (tt0) cc_final: 0.6897 (tt0) REVERT: A 255 ASP cc_start: 0.7418 (m-30) cc_final: 0.7191 (m-30) REVERT: D 85 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7767 (mtm) REVERT: B 139 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7272 (tp40) REVERT: B 287 ARG cc_start: 0.7143 (ttt-90) cc_final: 0.6868 (ttt-90) REVERT: B 462 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7356 (ttmm) REVERT: B 466 ASP cc_start: 0.7556 (m-30) cc_final: 0.7220 (m-30) REVERT: B 468 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6911 (mm-30) REVERT: C 77 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7652 (mtm180) REVERT: C 351 GLU cc_start: 0.7743 (mp0) cc_final: 0.7094 (mp0) REVERT: C 466 ASP cc_start: 0.7560 (m-30) cc_final: 0.7204 (m-30) outliers start: 50 outliers final: 25 residues processed: 327 average time/residue: 1.4114 time to fit residues: 501.6716 Evaluate side-chains 332 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 304 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 0.0070 chunk 185 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 70 GLN B 304 GLN B 447 ASN C 290 ASN C 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15570 Z= 0.211 Angle : 0.547 9.376 21084 Z= 0.280 Chirality : 0.043 0.137 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.383 19.724 2205 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.96 % Allowed : 13.74 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.27 (0.19), residues: 1932 helix: 1.85 (0.25), residues: 453 sheet: 0.65 (0.20), residues: 573 loop : 0.61 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 473 HIS 0.003 0.001 HIS D 30 PHE 0.013 0.001 PHE C 346 TYR 0.015 0.002 TYR A 294 ARG 0.012 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6536 (ttp-110) cc_final: 0.6173 (ttp-110) REVERT: A 193 GLU cc_start: 0.7058 (tt0) cc_final: 0.6800 (tt0) REVERT: A 255 ASP cc_start: 0.7357 (m-30) cc_final: 0.7136 (m-30) REVERT: B 287 ARG cc_start: 0.7129 (ttt-90) cc_final: 0.6858 (ttt-90) REVERT: B 462 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7358 (ttmm) REVERT: B 466 ASP cc_start: 0.7554 (m-30) cc_final: 0.7245 (m-30) REVERT: C 77 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7550 (mtm180) REVERT: C 351 GLU cc_start: 0.7760 (mp0) cc_final: 0.7059 (mp0) REVERT: C 466 ASP cc_start: 0.7594 (m-30) cc_final: 0.7199 (m-30) REVERT: C 468 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6852 (mm-30) REVERT: C 473 TRP cc_start: 0.6430 (m-10) cc_final: 0.6129 (m-90) REVERT: F 123 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7512 (tm-30) outliers start: 50 outliers final: 29 residues processed: 324 average time/residue: 1.4555 time to fit residues: 519.0595 Evaluate side-chains 330 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 300 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 70 GLN B 304 GLN ** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 180 ASN C 290 ASN C 418 ASN C 447 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15570 Z= 0.232 Angle : 0.557 9.925 21084 Z= 0.284 Chirality : 0.044 0.164 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.326 19.412 2205 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.66 % Allowed : 14.51 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.24 (0.19), residues: 1932 helix: 1.83 (0.25), residues: 459 sheet: 0.56 (0.20), residues: 570 loop : 0.64 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 473 HIS 0.003 0.001 HIS D 30 PHE 0.014 0.001 PHE C 346 TYR 0.015 0.002 TYR A 294 ARG 0.008 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 299 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6525 (ttp-110) cc_final: 0.6153 (ttp-110) REVERT: A 193 GLU cc_start: 0.7044 (tt0) cc_final: 0.6791 (tt0) REVERT: A 255 ASP cc_start: 0.7351 (m-30) cc_final: 0.7138 (m-30) REVERT: B 138 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7621 (OUTLIER) REVERT: B 156 LYS cc_start: 0.7991 (mttp) cc_final: 0.7727 (mtmm) REVERT: B 287 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6859 (ttt-90) REVERT: B 462 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7360 (ttmm) REVERT: B 466 ASP cc_start: 0.7558 (m-30) cc_final: 0.7241 (m-30) REVERT: C 351 GLU cc_start: 0.7759 (mp0) cc_final: 0.7022 (mp0) REVERT: C 466 ASP cc_start: 0.7599 (m-30) cc_final: 0.7183 (m-30) REVERT: C 468 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6860 (mm-30) REVERT: F 123 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7499 (tm-30) outliers start: 45 outliers final: 29 residues processed: 314 average time/residue: 1.3896 time to fit residues: 474.7972 Evaluate side-chains 328 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 299 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 0.1980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 418 ASN B 70 GLN B 304 GLN B 386 ASN B 418 ASN B 447 ASN C 180 ASN C 290 ASN C 447 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15570 Z= 0.179 Angle : 0.539 10.884 21084 Z= 0.275 Chirality : 0.043 0.191 2460 Planarity : 0.003 0.034 2700 Dihedral : 4.196 19.036 2205 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.31 % Allowed : 14.98 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.31 (0.19), residues: 1932 helix: 1.93 (0.25), residues: 459 sheet: 0.60 (0.20), residues: 570 loop : 0.66 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 473 HIS 0.006 0.001 HIS A 206 PHE 0.012 0.001 PHE B 346 TYR 0.013 0.001 TYR A 294 ARG 0.008 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 300 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6506 (ttp-110) cc_final: 0.6137 (ttp-110) REVERT: A 193 GLU cc_start: 0.7044 (tt0) cc_final: 0.6808 (tt0) REVERT: A 255 ASP cc_start: 0.7328 (m-30) cc_final: 0.7119 (m-30) REVERT: A 458 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 234 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 287 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6864 (ttt-90) REVERT: B 462 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7355 (ttmm) REVERT: B 466 ASP cc_start: 0.7558 (m-30) cc_final: 0.7242 (m-30) REVERT: C 351 GLU cc_start: 0.7752 (mp0) cc_final: 0.6996 (mp0) REVERT: C 466 ASP cc_start: 0.7650 (m-30) cc_final: 0.7252 (m-30) REVERT: C 469 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6509 (tt0) REVERT: C 473 TRP cc_start: 0.6405 (OUTLIER) cc_final: 0.6173 (m-90) REVERT: F 123 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7489 (tm-30) outliers start: 39 outliers final: 25 residues processed: 314 average time/residue: 1.3804 time to fit residues: 471.1616 Evaluate side-chains 324 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 294 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 473 TRP Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 75 optimal weight: 0.4980 chunk 135 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 70 GLN B 386 ASN B 418 ASN B 447 ASN C 290 ASN C 447 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15570 Z= 0.247 Angle : 0.568 11.990 21084 Z= 0.286 Chirality : 0.044 0.263 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.243 17.887 2205 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.19 % Allowed : 15.33 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.30 (0.19), residues: 1932 helix: 1.97 (0.25), residues: 459 sheet: 0.59 (0.20), residues: 570 loop : 0.61 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 473 HIS 0.004 0.001 HIS A 206 PHE 0.014 0.001 PHE C 346 TYR 0.015 0.002 TYR A 294 ARG 0.008 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 295 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6499 (ttp-110) cc_final: 0.6126 (ttp-110) REVERT: A 193 GLU cc_start: 0.7064 (tt0) cc_final: 0.6827 (tt0) REVERT: A 255 ASP cc_start: 0.7340 (m-30) cc_final: 0.7133 (m-30) REVERT: B 287 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6865 (ttt-90) REVERT: B 462 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7366 (ttmm) REVERT: B 466 ASP cc_start: 0.7565 (m-30) cc_final: 0.7238 (m-30) REVERT: C 351 GLU cc_start: 0.7764 (mp0) cc_final: 0.6992 (mp0) REVERT: C 466 ASP cc_start: 0.7656 (m-30) cc_final: 0.7217 (m-30) REVERT: C 473 TRP cc_start: 0.6412 (OUTLIER) cc_final: 0.6196 (m-90) REVERT: F 123 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7475 (tm-30) outliers start: 37 outliers final: 33 residues processed: 309 average time/residue: 1.4795 time to fit residues: 497.3406 Evaluate side-chains 327 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 292 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 473 TRP Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 0.1980 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 155 ASN B 304 GLN B 386 ASN B 418 ASN B 447 ASN C 418 ASN C 447 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15570 Z= 0.248 Angle : 0.570 12.762 21084 Z= 0.288 Chirality : 0.044 0.371 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.283 17.338 2205 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.13 % Allowed : 15.69 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.27 (0.19), residues: 1932 helix: 1.99 (0.25), residues: 459 sheet: 0.62 (0.21), residues: 549 loop : 0.54 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 473 HIS 0.004 0.001 HIS A 206 PHE 0.014 0.001 PHE C 346 TYR 0.016 0.002 TYR A 294 ARG 0.008 0.000 ARG C 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6462 (ttp-110) cc_final: 0.6095 (ttp-110) REVERT: A 193 GLU cc_start: 0.7066 (tt0) cc_final: 0.6826 (tt0) REVERT: A 255 ASP cc_start: 0.7344 (m-30) cc_final: 0.7134 (m-30) REVERT: B 287 ARG cc_start: 0.7126 (ttt-90) cc_final: 0.6863 (ttt-90) REVERT: B 462 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7388 (ttmm) REVERT: B 466 ASP cc_start: 0.7570 (m-30) cc_final: 0.7261 (m-30) REVERT: C 351 GLU cc_start: 0.7768 (mp0) cc_final: 0.6995 (mp0) REVERT: C 466 ASP cc_start: 0.7627 (m-30) cc_final: 0.7187 (m-30) REVERT: F 123 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7437 (tm-30) outliers start: 36 outliers final: 32 residues processed: 308 average time/residue: 1.4578 time to fit residues: 487.1469 Evaluate side-chains 322 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 289 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 0.0670 chunk 152 optimal weight: 0.0370 chunk 63 optimal weight: 0.9990 chunk 156 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 386 ASN B 418 ASN B 447 ASN C 155 ASN C 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116906 restraints weight = 20274.823| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.00 r_work: 0.3349 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15570 Z= 0.146 Angle : 0.546 12.601 21084 Z= 0.272 Chirality : 0.043 0.494 2460 Planarity : 0.003 0.034 2700 Dihedral : 4.192 28.199 2205 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.72 % Allowed : 16.10 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.43 (0.19), residues: 1932 helix: 1.95 (0.25), residues: 477 sheet: 0.86 (0.21), residues: 540 loop : 0.60 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP C 473 HIS 0.005 0.001 HIS A 206 PHE 0.013 0.001 PHE A 346 TYR 0.012 0.001 TYR A 294 ARG 0.008 0.000 ARG C 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7645.01 seconds wall clock time: 132 minutes 57.80 seconds (7977.80 seconds total)