Starting phenix.real_space_refine on Wed Aug 7 06:06:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/08_2024/8v5k_42983.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/08_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_42983/08_2024/8v5k_42983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/08_2024/8v5k_42983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/08_2024/8v5k_42983.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5k_42983/08_2024/8v5k_42983.cif" } 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-5409/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: 9.15, per 1000 atoms: 0.60 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: 6.29 Conformation dependent library (CDL) restraints added in 3.6 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: 2.45 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: 6.50 Time building geometry restraints manager: 6.91 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 3.040 nonbonded pdb=" OG SER H 55 " pdb=" OD1 ASN H 66 " model vdw 2.236 3.040 nonbonded pdb=" OG SER G 7 " pdb=" OG SER G 22 " model vdw 2.242 3.040 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.263 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 22 " model vdw 2.264 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 6.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 46.930 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.130 ------------------------------------------------------------------------------- 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 : 1.510 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: 1.4820 time to fit residues: 601.4584 Evaluate side-chains 312 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.075 ------------------------------------------------------------------------------- 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: 0.0470 chunk 145 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 304 GLN B 418 ASN C 290 ASN C 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15570 Z= 0.217 Angle : 0.607 10.261 21084 Z= 0.326 Chirality : 0.046 0.175 2460 Planarity : 0.004 0.034 2700 Dihedral : 5.142 32.751 2205 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.43 % Allowed : 8.82 % Favored : 88.75 % 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: 1.34 (0.19), residues: 1932 helix: 1.19 (0.24), residues: 453 sheet: 0.93 (0.21), residues: 561 loop : 0.90 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 473 HIS 0.005 0.001 HIS D 30 PHE 0.013 0.002 PHE C 111 TYR 0.018 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 360 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 319 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7428 (mm110) cc_final: 0.7192 (mm110) REVERT: A 136 GLU cc_start: 0.7410 (tt0) cc_final: 0.7154 (tt0) REVERT: A 189 ARG cc_start: 0.6386 (ttp-110) cc_final: 0.6123 (ttp-110) REVERT: A 193 GLU cc_start: 0.7198 (tt0) cc_final: 0.6952 (tt0) REVERT: A 462 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7568 (ttmm) REVERT: A 466 ASP cc_start: 0.7558 (m-30) cc_final: 0.7320 (m-30) REVERT: B 70 GLN cc_start: 0.7476 (mm110) cc_final: 0.7266 (mm-40) REVERT: B 287 ARG cc_start: 0.7115 (ttt-90) cc_final: 0.6843 (ttt-90) REVERT: B 462 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7569 (ttmm) REVERT: B 468 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6917 (mm-30) REVERT: C 466 ASP cc_start: 0.7457 (m-30) cc_final: 0.7173 (m-30) outliers start: 41 outliers final: 14 residues processed: 333 average time/residue: 1.5166 time to fit residues: 549.1633 Evaluate side-chains 320 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 306 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0050 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 447 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7510 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15570 Z= 0.228 Angle : 0.571 8.655 21084 Z= 0.300 Chirality : 0.045 0.143 2460 Planarity : 0.004 0.034 2700 Dihedral : 4.700 23.003 2205 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.72 % Allowed : 10.66 % Favored : 86.62 % 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: 1.42 (0.19), residues: 1932 helix: 1.60 (0.25), residues: 453 sheet: 0.81 (0.20), residues: 561 loop : 0.88 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 473 HIS 0.004 0.001 HIS D 30 PHE 0.014 0.002 PHE C 346 TYR 0.015 0.002 TYR I 117 ARG 0.009 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 354 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7414 (tt0) cc_final: 0.7115 (tt0) REVERT: A 189 ARG cc_start: 0.6479 (ttp-110) cc_final: 0.6150 (ttp-110) REVERT: A 193 GLU cc_start: 0.7141 (tt0) cc_final: 0.6887 (tt0) REVERT: A 466 ASP cc_start: 0.7584 (m-30) cc_final: 0.7384 (m-30) REVERT: G 117 TYR cc_start: 0.8580 (m-80) cc_final: 0.8114 (m-80) REVERT: B 24 LYS cc_start: 0.8091 (mtpm) cc_final: 0.7884 (mtpp) REVERT: B 70 GLN cc_start: 0.7442 (mm110) cc_final: 0.7229 (mm-40) REVERT: B 136 GLU cc_start: 0.7541 (tt0) cc_final: 0.7291 (tt0) REVERT: B 189 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.6376 (ttp-110) REVERT: B 287 ARG cc_start: 0.7123 (ttt-90) cc_final: 0.6849 (ttt-90) REVERT: B 462 LYS cc_start: 0.7746 (ttmm) cc_final: 0.7390 (ttmm) REVERT: B 466 ASP cc_start: 0.7478 (m-30) cc_final: 0.7253 (m-30) REVERT: C 466 ASP cc_start: 0.7509 (m-30) cc_final: 0.7203 (m-30) outliers start: 46 outliers final: 14 residues processed: 328 average time/residue: 1.4706 time to fit residues: 523.7489 Evaluate side-chains 320 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 306 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 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 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 E residue 39 MET 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: 3.9990 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 166 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 447 ASN C 42 GLN C 290 ASN C 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15570 Z= 0.392 Angle : 0.620 11.158 21084 Z= 0.321 Chirality : 0.047 0.184 2460 Planarity : 0.004 0.038 2700 Dihedral : 4.713 21.271 2205 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.90 % Allowed : 11.84 % Favored : 85.26 % 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: 1.65 (0.25), residues: 453 sheet: 0.66 (0.20), residues: 573 loop : 0.67 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 473 HIS 0.005 0.001 HIS D 30 PHE 0.019 0.002 PHE C 346 TYR 0.019 0.002 TYR B 294 ARG 0.007 0.001 ARG C 306 *********************** 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 356 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 307 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6495 (ttp-110) cc_final: 0.6161 (ttp-110) REVERT: A 193 GLU cc_start: 0.7162 (tt0) cc_final: 0.6913 (tt0) REVERT: A 466 ASP cc_start: 0.7626 (m-30) cc_final: 0.7425 (m-30) REVERT: B 24 LYS cc_start: 0.8129 (mtpm) cc_final: 0.7882 (mtpp) REVERT: B 70 GLN cc_start: 0.7559 (mm110) cc_final: 0.7337 (mm-40) REVERT: B 136 GLU cc_start: 0.7597 (tt0) cc_final: 0.7316 (tt0) REVERT: B 287 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6888 (ttt-90) REVERT: B 462 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7386 (ttmm) REVERT: B 466 ASP cc_start: 0.7510 (m-30) cc_final: 0.7244 (m-30) REVERT: C 351 GLU cc_start: 0.7738 (mp0) cc_final: 0.7116 (mp0) REVERT: C 466 ASP cc_start: 0.7552 (m-30) cc_final: 0.7241 (m-30) outliers start: 49 outliers final: 20 residues processed: 327 average time/residue: 1.4467 time to fit residues: 514.5881 Evaluate side-chains 326 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 306 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 SER 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 314 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 432 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 0.0970 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 304 GLN B 447 ASN C 42 GLN C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15570 Z= 0.206 Angle : 0.549 9.890 21084 Z= 0.285 Chirality : 0.044 0.139 2460 Planarity : 0.004 0.034 2700 Dihedral : 4.466 20.710 2205 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.25 % Allowed : 13.32 % Favored : 84.43 % 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: 1.81 (0.25), residues: 453 sheet: 0.67 (0.20), residues: 561 loop : 0.65 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 0.007 0.000 ARG C 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 340 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 302 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6533 (ttp-110) cc_final: 0.6184 (ttp-110) REVERT: A 193 GLU cc_start: 0.7111 (tt0) cc_final: 0.6876 (tt0) REVERT: A 466 ASP cc_start: 0.7629 (m-30) cc_final: 0.7351 (m-30) REVERT: B 136 GLU cc_start: 0.7539 (tt0) cc_final: 0.7258 (tt0) REVERT: B 287 ARG cc_start: 0.7142 (ttt-90) cc_final: 0.6870 (ttt-90) REVERT: B 462 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7386 (ttmm) REVERT: B 466 ASP cc_start: 0.7526 (m-30) cc_final: 0.7263 (m-30) REVERT: C 351 GLU cc_start: 0.7752 (mp0) cc_final: 0.7150 (mp0) REVERT: C 466 ASP cc_start: 0.7545 (m-30) cc_final: 0.7235 (m-30) REVERT: C 468 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6848 (mm-30) outliers start: 38 outliers final: 21 residues processed: 319 average time/residue: 1.4887 time to fit residues: 515.4910 Evaluate side-chains 313 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 292 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER 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 402 ASN Chi-restraints excluded: chain B residue 407 GLN 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 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU 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: 3.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 0.0470 chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 290 ASN B 304 GLN B 447 ASN C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15570 Z= 0.256 Angle : 0.568 9.709 21084 Z= 0.291 Chirality : 0.044 0.168 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.407 20.396 2205 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.96 % Allowed : 13.50 % Favored : 83.54 % 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: 1.86 (0.25), residues: 453 sheet: 0.65 (0.20), residues: 561 loop : 0.62 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 473 HIS 0.004 0.001 HIS D 30 PHE 0.015 0.002 PHE C 346 TYR 0.015 0.002 TYR A 294 ARG 0.013 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 361 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 311 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6531 (ttp-110) cc_final: 0.6176 (ttp-110) REVERT: A 193 GLU cc_start: 0.7062 (tt0) cc_final: 0.6835 (tt0) REVERT: A 466 ASP cc_start: 0.7639 (m-30) cc_final: 0.7423 (m-30) REVERT: B 24 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7859 (mtpm) REVERT: B 136 GLU cc_start: 0.7550 (tt0) cc_final: 0.7270 (tt0) REVERT: B 287 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6886 (ttt-90) REVERT: B 462 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7393 (ttmm) REVERT: B 466 ASP cc_start: 0.7538 (m-30) cc_final: 0.7268 (m-30) REVERT: C 270 ASP cc_start: 0.7823 (t0) cc_final: 0.7593 (t0) REVERT: C 351 GLU cc_start: 0.7774 (mp0) cc_final: 0.7145 (mp0) REVERT: C 468 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6857 (mm-30) outliers start: 50 outliers final: 29 residues processed: 329 average time/residue: 1.4704 time to fit residues: 526.9632 Evaluate side-chains 330 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 301 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS 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 G residue 7 SER 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 190 LEU Chi-restraints excluded: chain B residue 234 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 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 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 113 THR 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: 0.9990 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 185 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 290 ASN B 304 GLN B 447 ASN C 180 ASN C 399 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15570 Z= 0.212 Angle : 0.560 10.944 21084 Z= 0.286 Chirality : 0.043 0.176 2460 Planarity : 0.003 0.034 2700 Dihedral : 4.317 20.053 2205 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.61 % Allowed : 14.21 % Favored : 83.19 % 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: 2.00 (0.25), residues: 453 sheet: 0.65 (0.20), residues: 561 loop : 0.64 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 473 HIS 0.003 0.001 HIS A 206 PHE 0.013 0.001 PHE C 346 TYR 0.014 0.001 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 347 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6519 (ttp-110) cc_final: 0.6151 (ttp-110) REVERT: A 193 GLU cc_start: 0.7029 (tt0) cc_final: 0.6777 (tt0) REVERT: A 466 ASP cc_start: 0.7637 (m-30) cc_final: 0.7423 (m-30) REVERT: B 136 GLU cc_start: 0.7533 (tt0) cc_final: 0.7265 (tt0) REVERT: B 287 ARG cc_start: 0.7149 (ttt-90) cc_final: 0.6883 (ttt-90) REVERT: B 462 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7379 (ttmm) REVERT: B 466 ASP cc_start: 0.7544 (m-30) cc_final: 0.7254 (m-30) REVERT: C 351 GLU cc_start: 0.7795 (mp0) cc_final: 0.7140 (mp0) REVERT: C 468 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6853 (mm-30) REVERT: C 473 TRP cc_start: 0.6423 (m-10) cc_final: 0.6145 (m-90) outliers start: 44 outliers final: 28 residues processed: 319 average time/residue: 1.4459 time to fit residues: 501.6732 Evaluate side-chains 334 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 306 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 G residue 7 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER 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 402 ASN Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU 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 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 113 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 290 ASN B 304 GLN B 447 ASN C 180 ASN C 399 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15570 Z= 0.243 Angle : 0.571 12.716 21084 Z= 0.291 Chirality : 0.044 0.223 2460 Planarity : 0.004 0.034 2700 Dihedral : 4.309 19.201 2205 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.19 % Allowed : 15.57 % Favored : 82.24 % 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: 1.32 (0.19), residues: 1932 helix: 1.98 (0.25), residues: 459 sheet: 0.64 (0.20), residues: 561 loop : 0.60 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 473 HIS 0.003 0.001 HIS D 30 PHE 0.015 0.002 PHE C 346 TYR 0.015 0.002 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 337 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 300 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6497 (ttp-110) cc_final: 0.6129 (ttp-110) REVERT: A 193 GLU cc_start: 0.7078 (tt0) cc_final: 0.6825 (tt0) REVERT: A 435 LEU cc_start: 0.8183 (tp) cc_final: 0.7860 (tp) REVERT: A 466 ASP cc_start: 0.7642 (m-30) cc_final: 0.7428 (m-30) REVERT: B 136 GLU cc_start: 0.7532 (tt0) cc_final: 0.7293 (tt0) REVERT: B 287 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6883 (ttt-90) REVERT: B 462 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7381 (ttmm) REVERT: B 466 ASP cc_start: 0.7547 (m-30) cc_final: 0.7249 (m-30) REVERT: B 471 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7604 (mttm) REVERT: C 351 GLU cc_start: 0.7808 (mp0) cc_final: 0.7141 (mp0) REVERT: C 466 ASP cc_start: 0.7610 (m-30) cc_final: 0.7153 (m-30) REVERT: C 468 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6863 (mm-30) outliers start: 37 outliers final: 35 residues processed: 315 average time/residue: 1.4359 time to fit residues: 493.2978 Evaluate side-chains 336 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 301 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 88 LEU 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 393 THR Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 ILE 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 407 GLN Chi-restraints excluded: chain B residue 432 GLU 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 261 SER 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 E residue 113 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.6980 chunk 161 optimal weight: 0.0470 chunk 172 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 399 ASN A 418 ASN B 70 GLN B 290 ASN B 304 GLN B 418 ASN B 447 ASN C 399 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2366 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= 0.207 Angle : 0.563 13.393 21084 Z= 0.287 Chirality : 0.044 0.231 2460 Planarity : 0.004 0.033 2700 Dihedral : 4.263 18.867 2205 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.37 % Allowed : 16.04 % Favored : 81.59 % 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: 1.34 (0.19), residues: 1932 helix: 2.02 (0.25), residues: 459 sheet: 0.67 (0.20), residues: 561 loop : 0.60 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP C 473 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE C 346 TYR 0.013 0.001 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 339 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6475 (ttp-110) cc_final: 0.6121 (ttp-110) REVERT: A 193 GLU cc_start: 0.7066 (tt0) cc_final: 0.6823 (tt0) REVERT: A 466 ASP cc_start: 0.7642 (m-30) cc_final: 0.7427 (m-30) REVERT: B 136 GLU cc_start: 0.7492 (tt0) cc_final: 0.7241 (tt0) REVERT: B 234 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7655 (tt) REVERT: B 287 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.6874 (ttt-90) REVERT: B 462 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7380 (ttmm) REVERT: B 466 ASP cc_start: 0.7548 (m-30) cc_final: 0.7249 (m-30) REVERT: C 351 GLU cc_start: 0.7800 (mp0) cc_final: 0.7106 (mp0) REVERT: C 466 ASP cc_start: 0.7675 (m-30) cc_final: 0.7205 (m-30) outliers start: 40 outliers final: 33 residues processed: 315 average time/residue: 1.4058 time to fit residues: 482.5426 Evaluate side-chains 339 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 305 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain G residue 7 SER 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 190 LEU Chi-restraints excluded: chain B residue 213 ILE 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 317 MET 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 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 261 SER 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 E residue 113 THR Chi-restraints excluded: chain H residue 28 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.0050 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 0.0030 chunk 15 optimal weight: 0.1980 chunk 117 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 overall best weight: 0.2204 ------------------------------------------------------------------------------- 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 A 399 ASN A 418 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN C 447 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 15570 Z= 0.147 Angle : 0.542 13.549 21084 Z= 0.275 Chirality : 0.043 0.232 2460 Planarity : 0.003 0.033 2700 Dihedral : 4.123 18.755 2205 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.78 % Allowed : 16.34 % Favored : 81.88 % 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: 1.45 (0.19), residues: 1932 helix: 2.00 (0.24), residues: 477 sheet: 0.80 (0.21), residues: 540 loop : 0.65 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 473 HIS 0.005 0.001 HIS C 206 PHE 0.012 0.001 PHE B 346 TYR 0.011 0.001 TYR A 294 ARG 0.007 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 360 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 330 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6461 (ttp-110) cc_final: 0.6093 (ttp-110) REVERT: A 193 GLU cc_start: 0.6995 (tt0) cc_final: 0.6789 (tt0) REVERT: A 351 GLU cc_start: 0.7654 (mp0) cc_final: 0.7434 (mp0) REVERT: A 435 LEU cc_start: 0.8192 (tp) cc_final: 0.7909 (tp) REVERT: A 466 ASP cc_start: 0.7628 (m-30) cc_final: 0.7415 (m-30) REVERT: B 234 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 287 ARG cc_start: 0.7032 (ttt-90) cc_final: 0.6755 (ttt-90) REVERT: B 462 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7369 (ttmm) REVERT: B 466 ASP cc_start: 0.7542 (m-30) cc_final: 0.7239 (m-30) REVERT: C 351 GLU cc_start: 0.7786 (mp0) cc_final: 0.7114 (mp0) REVERT: C 466 ASP cc_start: 0.7641 (m-30) cc_final: 0.7181 (m-30) outliers start: 30 outliers final: 20 residues processed: 344 average time/residue: 1.3970 time to fit residues: 523.1976 Evaluate side-chains 339 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 318 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 432 GLU 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 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 28 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: 0.8980 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 152 optimal weight: 0.0010 chunk 63 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 399 ASN A 418 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN C 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114016 restraints weight = 20383.195| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.02 r_work: 0.3337 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15570 Z= 0.176 Angle : 0.568 13.338 21084 Z= 0.285 Chirality : 0.044 0.427 2460 Planarity : 0.004 0.033 2700 Dihedral : 4.129 19.746 2205 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 17.11 % Favored : 81.17 % 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: 1.49 (0.19), residues: 1932 helix: 2.03 (0.24), residues: 477 sheet: 0.86 (0.21), residues: 540 loop : 0.65 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 473 HIS 0.004 0.001 HIS C 206 PHE 0.012 0.001 PHE B 346 TYR 0.016 0.001 TYR B 274 ARG 0.011 0.000 ARG B 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7848.62 seconds wall clock time: 137 minutes 33.87 seconds (8253.87 seconds total)