Starting phenix.real_space_refine on Sat Feb 17 08:28:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpt_30810/02_2024/7dpt_30810_updated.pdb" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 88 5.16 5 C 11256 2.51 5 N 3132 2.21 5 O 3528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 390": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D GLU 528": "OE1" <-> "OE2" Residue "D ARG 532": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18052 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "B" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "C" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "D" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {' MG': 4, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {' MG': 2, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {' MG': 4, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {' MG': 2, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 9.92, per 1000 atoms: 0.55 Number of scatterers: 18052 At special positions: 0 Unit cell: (128.26, 98.58, 128.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 36 15.00 Mg 12 11.99 O 3528 8.00 N 3132 7.00 C 11256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 3.4 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 16 sheets defined 42.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 52 through 55 No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 113 through 129 removed outlier: 7.339A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.797A pdb=" N MET A 156 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 3.989A pdb=" N GLN A 166 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.729A pdb=" N CYS A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 249 through 259 Proline residue: A 253 - end of helix removed outlier: 3.594A pdb=" N GLN A 258 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.648A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 removed outlier: 3.524A pdb=" N ALA A 315 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 326 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 Processing helix chain 'A' and resid 344 through 347 No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.982A pdb=" N ARG A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 413 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 487 through 493 removed outlier: 4.309A pdb=" N HIS A 490 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 538 through 548 Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 113 through 129 removed outlier: 7.339A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.797A pdb=" N MET B 156 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Proline residue: B 157 - end of helix removed outlier: 3.989A pdb=" N GLN B 166 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.729A pdb=" N CYS B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 249 through 259 Proline residue: B 253 - end of helix removed outlier: 3.594A pdb=" N GLN B 258 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.648A pdb=" N GLU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 removed outlier: 3.524A pdb=" N ALA B 315 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER B 316 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 326 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 344 through 347 No H-bonds generated for 'chain 'B' and resid 344 through 347' Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 378 through 390 removed outlier: 3.982A pdb=" N ARG B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 413 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 487 through 493 removed outlier: 4.309A pdb=" N HIS B 490 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 551 through 555 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.339A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 168 removed outlier: 3.797A pdb=" N MET C 156 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Proline residue: C 157 - end of helix removed outlier: 3.989A pdb=" N GLN C 166 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.729A pdb=" N CYS C 206 " --> pdb=" O GLU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 249 through 259 Proline residue: C 253 - end of helix removed outlier: 3.594A pdb=" N GLN C 258 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 283 through 293 removed outlier: 3.648A pdb=" N GLU C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.524A pdb=" N ALA C 315 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 316 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 326 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 344 through 347 No H-bonds generated for 'chain 'C' and resid 344 through 347' Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.982A pdb=" N ARG C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 413 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 487 through 493 removed outlier: 4.309A pdb=" N HIS C 490 " --> pdb=" O LYS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 538 through 548 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'D' and resid 16 through 29 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 52 through 55 No H-bonds generated for 'chain 'D' and resid 52 through 55' Processing helix chain 'D' and resid 69 through 78 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 113 through 129 removed outlier: 7.339A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 168 removed outlier: 3.797A pdb=" N MET D 156 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Proline residue: D 157 - end of helix removed outlier: 3.989A pdb=" N GLN D 166 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.729A pdb=" N CYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 249 through 259 Proline residue: D 253 - end of helix removed outlier: 3.594A pdb=" N GLN D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 283 through 293 removed outlier: 3.648A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 removed outlier: 3.524A pdb=" N ALA D 315 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER D 316 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU D 326 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 342 Processing helix chain 'D' and resid 344 through 347 No H-bonds generated for 'chain 'D' and resid 344 through 347' Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 378 through 390 removed outlier: 3.982A pdb=" N ARG D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 413 Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 463 through 467 Processing helix chain 'D' and resid 487 through 493 removed outlier: 4.309A pdb=" N HIS D 490 " --> pdb=" O LYS D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 529 No H-bonds generated for 'chain 'D' and resid 527 through 529' Processing helix chain 'D' and resid 538 through 548 Processing helix chain 'D' and resid 551 through 555 Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.175A pdb=" N ILE A 213 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 243 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS A 215 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 3 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA A 177 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 5 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 179 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 7 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU A 181 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY A 8 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 332 through 338 removed outlier: 6.462A pdb=" N VAL A 299 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 335 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 301 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE A 337 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 303 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY A 366 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 304 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 368 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 433 through 435 Processing sheet with id= D, first strand: chain 'A' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL A 474 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.175A pdb=" N ILE B 213 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE B 243 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS B 215 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 3 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA B 177 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 5 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 179 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 7 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU B 181 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 8 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 332 through 338 removed outlier: 6.462A pdb=" N VAL B 299 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL B 335 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 301 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 337 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL B 303 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY B 366 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 304 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 368 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 433 through 435 Processing sheet with id= H, first strand: chain 'B' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL B 474 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 240 through 244 removed outlier: 6.175A pdb=" N ILE C 213 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE C 243 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS C 215 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 3 " --> pdb=" O CYS C 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA C 177 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 5 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 179 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR C 7 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU C 181 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY C 8 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 332 through 338 removed outlier: 6.462A pdb=" N VAL C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL C 335 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE C 301 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL C 304 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU C 368 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 433 through 435 Processing sheet with id= L, first strand: chain 'C' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL C 474 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.175A pdb=" N ILE D 213 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE D 243 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS D 215 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR D 3 " --> pdb=" O CYS D 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA D 177 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU D 5 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL D 179 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 7 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU D 181 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY D 8 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 332 through 338 removed outlier: 6.462A pdb=" N VAL D 299 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL D 335 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 301 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY D 366 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL D 304 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU D 368 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 433 through 435 Processing sheet with id= P, first strand: chain 'D' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL D 474 " --> pdb=" O THR D 455 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1512 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: 6.09 Time building geometry restraints manager: 7.65 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: 5880 1.34 - 1.46: 2644 1.46 - 1.57: 9608 1.57 - 1.69: 60 1.69 - 1.81: 124 Bond restraints: 18316 Sorted by residual: bond pdb=" C23 5ZL A 708 " pdb=" O04 5ZL A 708 " ideal model delta sigma weight residual 1.275 1.496 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C23 5ZL C 708 " pdb=" O04 5ZL C 708 " ideal model delta sigma weight residual 1.275 1.496 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C23 5ZL B 706 " pdb=" O04 5ZL B 706 " ideal model delta sigma weight residual 1.275 1.496 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C23 5ZL D 706 " pdb=" O04 5ZL D 706 " ideal model delta sigma weight residual 1.275 1.496 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C27 5ZL B 706 " pdb=" N19 5ZL B 706 " ideal model delta sigma weight residual 1.312 1.452 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 18311 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.46: 616 106.46 - 113.73: 10360 113.73 - 120.99: 8464 120.99 - 128.26: 5252 128.26 - 135.52: 184 Bond angle restraints: 24876 Sorted by residual: angle pdb=" PA ADP B 703 " pdb=" O3A ADP B 703 " pdb=" PB ADP B 703 " ideal model delta sigma weight residual 120.50 135.52 -15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" PA ADP D 703 " pdb=" O3A ADP D 703 " pdb=" PB ADP D 703 " ideal model delta sigma weight residual 120.50 135.52 -15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" PA ADP A 703 " pdb=" O3A ADP A 703 " pdb=" PB ADP A 703 " ideal model delta sigma weight residual 120.50 135.52 -15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" PA ADP C 703 " pdb=" O3A ADP C 703 " pdb=" PB ADP C 703 " ideal model delta sigma weight residual 120.50 135.52 -15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" CA DON C 702 " pdb=" C DON C 702 " pdb=" O DON C 702 " ideal model delta sigma weight residual 120.80 128.34 -7.54 1.70e+00 3.46e-01 1.97e+01 ... (remaining 24871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 10432 31.02 - 62.03: 508 62.03 - 93.05: 46 93.05 - 124.06: 4 124.06 - 155.08: 10 Dihedral angle restraints: 11000 sinusoidal: 4608 harmonic: 6392 Sorted by residual: dihedral pdb=" O2A ADP D 703 " pdb=" O3A ADP D 703 " pdb=" PA ADP D 703 " pdb=" PB ADP D 703 " ideal model delta sinusoidal sigma weight residual -60.00 95.08 -155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP C 703 " pdb=" O3A ADP C 703 " pdb=" PA ADP C 703 " pdb=" PB ADP C 703 " ideal model delta sinusoidal sigma weight residual -60.00 95.08 -155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' ADP C 703 " pdb=" O5' ADP C 703 " pdb=" PA ADP C 703 " pdb=" O2A ADP C 703 " ideal model delta sinusoidal sigma weight residual 300.00 162.88 137.12 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 10997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1784 0.040 - 0.079: 708 0.079 - 0.119: 252 0.119 - 0.158: 32 0.158 - 0.198: 4 Chirality restraints: 2780 Sorted by residual: chirality pdb=" C3' ADP B 703 " pdb=" C2' ADP B 703 " pdb=" C4' ADP B 703 " pdb=" O3' ADP B 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C3' ADP D 703 " pdb=" C2' ADP D 703 " pdb=" C4' ADP D 703 " pdb=" O3' ADP D 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C3' ADP A 703 " pdb=" C2' ADP A 703 " pdb=" C4' ADP A 703 " pdb=" O3' ADP A 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 2777 not shown) Planarity restraints: 3156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 369 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 370 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 369 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 370 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 369 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 370 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " -0.025 5.00e-02 4.00e+02 ... (remaining 3153 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.14: 24 2.14 - 2.83: 5508 2.83 - 3.52: 24332 3.52 - 4.21: 45824 4.21 - 4.90: 79272 Nonbonded interactions: 154960 Sorted by model distance: nonbonded pdb=" OD2 ASP C 70 " pdb=" O HOH C 801 " model vdw 1.445 2.440 nonbonded pdb=" OD2 ASP A 70 " pdb=" O HOH A 801 " model vdw 1.445 2.440 nonbonded pdb=" OD2 ASP B 70 " pdb=" O HOH B 801 " model vdw 1.445 2.440 nonbonded pdb=" OD2 ASP D 70 " pdb=" O HOH D 801 " model vdw 1.445 2.440 nonbonded pdb=" O3B ADP C 703 " pdb=" O HOH C 801 " model vdw 1.833 2.440 ... (remaining 154955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 556 or resid 701 through 705)) selection = (chain 'B' and (resid 1 through 556 or resid 701 through 705)) selection = (chain 'C' and (resid 1 through 556 or resid 701 through 705)) selection = (chain 'D' and (resid 1 through 556 or resid 701 through 705)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.020 Extract box with map and model: 4.330 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.230 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.009 0.221 18316 Z= 0.592 Angle : 0.844 15.020 24876 Z= 0.385 Chirality : 0.047 0.198 2780 Planarity : 0.004 0.045 3156 Dihedral : 18.065 155.078 6904 Min Nonbonded Distance : 1.445 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.23 % Allowed : 17.49 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -3.03 (0.15), residues: 2216 helix: -1.94 (0.14), residues: 908 sheet: -0.60 (0.25), residues: 376 loop : -2.60 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 124 HIS 0.003 0.001 HIS C 116 PHE 0.010 0.001 PHE D 162 TYR 0.013 0.001 TYR D 106 ARG 0.001 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 310 time to evaluate : 1.998 Fit side-chains REVERT: A 219 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7630 (mttm) REVERT: A 287 ASP cc_start: 0.8015 (m-30) cc_final: 0.7666 (m-30) REVERT: A 550 ARG cc_start: 0.7313 (mmt-90) cc_final: 0.7060 (mmp80) REVERT: B 263 GLU cc_start: 0.7741 (mp0) cc_final: 0.7525 (mm-30) REVERT: B 276 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.7361 (m) REVERT: B 550 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.7034 (mmp80) REVERT: C 263 GLU cc_start: 0.7757 (mp0) cc_final: 0.7503 (mm-30) REVERT: C 276 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7343 (m) REVERT: C 287 ASP cc_start: 0.8006 (m-30) cc_final: 0.7671 (m-30) REVERT: C 550 ARG cc_start: 0.7314 (mmt-90) cc_final: 0.7028 (mmp80) REVERT: D 219 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7626 (mttm) REVERT: D 287 ASP cc_start: 0.7993 (m-30) cc_final: 0.7653 (m-30) REVERT: D 550 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.7012 (mmp80) outliers start: 24 outliers final: 0 residues processed: 322 average time/residue: 1.6149 time to fit residues: 570.3358 Evaluate side-chains 247 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 172 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 199 optimal weight: 0.0870 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18316 Z= 0.157 Angle : 0.604 6.673 24876 Z= 0.290 Chirality : 0.045 0.126 2780 Planarity : 0.005 0.042 3156 Dihedral : 11.617 146.240 2562 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.16 % Favored : 96.66 % Rotamer: Outliers : 2.11 % Allowed : 21.55 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2216 helix: -0.40 (0.17), residues: 900 sheet: 0.11 (0.25), residues: 372 loop : -1.68 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.003 0.001 HIS B 480 PHE 0.007 0.001 PHE A 162 TYR 0.011 0.001 TYR A 42 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 2.139 Fit side-chains REVERT: A 411 ARG cc_start: 0.6707 (ptp-170) cc_final: 0.6423 (ptp-170) REVERT: A 550 ARG cc_start: 0.7211 (mmt-90) cc_final: 0.6962 (mmp80) REVERT: B 263 GLU cc_start: 0.7789 (mp0) cc_final: 0.7537 (mm-30) REVERT: B 363 ASP cc_start: 0.6932 (p0) cc_final: 0.6621 (p0) REVERT: B 550 ARG cc_start: 0.7231 (mmt-90) cc_final: 0.6950 (mmp80) REVERT: C 363 ASP cc_start: 0.6904 (p0) cc_final: 0.6615 (p0) REVERT: C 378 MET cc_start: 0.7277 (tpp) cc_final: 0.7067 (mmm) REVERT: C 411 ARG cc_start: 0.6703 (ptp-170) cc_final: 0.6413 (ptp-170) REVERT: D 363 ASP cc_start: 0.6923 (p0) cc_final: 0.6632 (p0) REVERT: D 411 ARG cc_start: 0.6697 (ptp-170) cc_final: 0.6406 (ptp-170) REVERT: D 448 MET cc_start: 0.7787 (mtt) cc_final: 0.7502 (mtt) REVERT: D 550 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6932 (mmp80) outliers start: 41 outliers final: 10 residues processed: 294 average time/residue: 1.4375 time to fit residues: 468.7096 Evaluate side-chains 245 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 505 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 HIS D 480 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18316 Z= 0.207 Angle : 0.632 7.009 24876 Z= 0.305 Chirality : 0.045 0.135 2780 Planarity : 0.005 0.046 3156 Dihedral : 11.727 155.377 2560 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 3.29 % Allowed : 20.42 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.59 (0.18), residues: 2216 helix: 0.14 (0.18), residues: 884 sheet: 0.34 (0.25), residues: 376 loop : -1.14 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 124 HIS 0.005 0.001 HIS A 116 PHE 0.016 0.001 PHE D 162 TYR 0.013 0.001 TYR B 106 ARG 0.003 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 243 time to evaluate : 2.218 Fit side-chains REVERT: A 379 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5541 (tp30) REVERT: A 411 ARG cc_start: 0.6645 (ptp-170) cc_final: 0.6395 (ptp-170) REVERT: A 550 ARG cc_start: 0.7228 (mmt-90) cc_final: 0.6981 (mmp80) REVERT: B 263 GLU cc_start: 0.7858 (mp0) cc_final: 0.7448 (mm-30) REVERT: B 363 ASP cc_start: 0.7204 (p0) cc_final: 0.6901 (p0) REVERT: B 448 MET cc_start: 0.7661 (mtm) cc_final: 0.7379 (mtt) REVERT: B 550 ARG cc_start: 0.7232 (mmt-90) cc_final: 0.6949 (mmp80) REVERT: C 363 ASP cc_start: 0.7166 (p0) cc_final: 0.6883 (p0) REVERT: D 363 ASP cc_start: 0.7183 (p0) cc_final: 0.6899 (p0) REVERT: D 448 MET cc_start: 0.7845 (mtt) cc_final: 0.7616 (mtt) REVERT: D 550 ARG cc_start: 0.7209 (mmt-90) cc_final: 0.6926 (mmp80) outliers start: 64 outliers final: 24 residues processed: 287 average time/residue: 1.4152 time to fit residues: 450.9530 Evaluate side-chains 254 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18316 Z= 0.175 Angle : 0.607 6.487 24876 Z= 0.292 Chirality : 0.045 0.129 2780 Planarity : 0.005 0.046 3156 Dihedral : 11.732 163.482 2560 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 3.24 % Allowed : 21.55 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.29 (0.18), residues: 2216 helix: 0.38 (0.18), residues: 880 sheet: 0.43 (0.25), residues: 392 loop : -0.93 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 124 HIS 0.004 0.001 HIS A 116 PHE 0.012 0.001 PHE A 162 TYR 0.012 0.001 TYR C 106 ARG 0.003 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 228 time to evaluate : 2.132 Fit side-chains REVERT: A 379 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5522 (tp30) REVERT: A 550 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.6939 (mmp80) REVERT: B 263 GLU cc_start: 0.7874 (mp0) cc_final: 0.7485 (mm-30) REVERT: B 275 MET cc_start: 0.6598 (mmt) cc_final: 0.6360 (mmt) REVERT: B 379 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5903 (tt0) REVERT: B 448 MET cc_start: 0.7674 (mtm) cc_final: 0.7383 (mtt) REVERT: B 550 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6907 (mmp80) REVERT: C 363 ASP cc_start: 0.7217 (p0) cc_final: 0.6925 (p0) REVERT: D 156 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7400 (tpt) REVERT: D 363 ASP cc_start: 0.7234 (p0) cc_final: 0.6946 (p0) REVERT: D 379 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5984 (tt0) REVERT: D 448 MET cc_start: 0.7838 (mtt) cc_final: 0.7606 (mtt) REVERT: D 550 ARG cc_start: 0.7166 (mmt-90) cc_final: 0.6888 (mmp80) outliers start: 63 outliers final: 26 residues processed: 274 average time/residue: 1.3936 time to fit residues: 425.6293 Evaluate side-chains 252 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18316 Z= 0.186 Angle : 0.610 6.653 24876 Z= 0.293 Chirality : 0.045 0.131 2780 Planarity : 0.005 0.046 3156 Dihedral : 11.831 171.004 2560 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 3.19 % Allowed : 21.81 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.16 (0.18), residues: 2216 helix: 0.48 (0.18), residues: 876 sheet: 0.48 (0.25), residues: 400 loop : -0.85 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 124 HIS 0.005 0.001 HIS A 116 PHE 0.013 0.001 PHE D 162 TYR 0.012 0.001 TYR B 106 ARG 0.003 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 218 time to evaluate : 1.968 Fit side-chains REVERT: A 550 ARG cc_start: 0.7234 (mmt-90) cc_final: 0.6989 (mmp80) REVERT: B 379 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5935 (tt0) REVERT: B 448 MET cc_start: 0.7697 (mtm) cc_final: 0.7405 (mtt) REVERT: B 550 ARG cc_start: 0.7239 (mmt-90) cc_final: 0.6955 (mmp80) REVERT: C 379 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5925 (tp30) REVERT: D 156 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7413 (tpt) REVERT: D 363 ASP cc_start: 0.7317 (p0) cc_final: 0.7027 (p0) REVERT: D 379 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6077 (tt0) REVERT: D 448 MET cc_start: 0.7834 (mtt) cc_final: 0.7603 (mtt) REVERT: D 550 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6912 (mmp80) outliers start: 62 outliers final: 29 residues processed: 270 average time/residue: 1.3649 time to fit residues: 411.1031 Evaluate side-chains 247 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18316 Z= 0.233 Angle : 0.643 7.136 24876 Z= 0.309 Chirality : 0.046 0.138 2780 Planarity : 0.005 0.047 3156 Dihedral : 11.996 173.154 2560 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % Rotamer: Outliers : 2.78 % Allowed : 22.22 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.18 (0.18), residues: 2216 helix: 0.45 (0.18), residues: 880 sheet: 0.45 (0.25), residues: 404 loop : -0.84 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 124 HIS 0.006 0.001 HIS A 116 PHE 0.016 0.001 PHE D 162 TYR 0.013 0.001 TYR D 106 ARG 0.005 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 2.127 Fit side-chains REVERT: A 54 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: A 550 ARG cc_start: 0.7236 (mmt-90) cc_final: 0.6983 (mmp80) REVERT: B 54 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: B 379 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5993 (tt0) REVERT: B 448 MET cc_start: 0.7708 (mtm) cc_final: 0.7416 (mtt) REVERT: B 550 ARG cc_start: 0.7244 (mmt-90) cc_final: 0.6949 (mmp80) REVERT: C 54 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: C 379 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6001 (tp30) REVERT: D 156 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7443 (tpt) REVERT: D 379 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6067 (tt0) REVERT: D 448 MET cc_start: 0.7780 (mtt) cc_final: 0.7576 (mtt) REVERT: D 550 ARG cc_start: 0.7239 (mmt-90) cc_final: 0.6926 (mmp80) outliers start: 54 outliers final: 32 residues processed: 266 average time/residue: 1.4074 time to fit residues: 416.9241 Evaluate side-chains 255 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18316 Z= 0.150 Angle : 0.580 6.381 24876 Z= 0.277 Chirality : 0.044 0.123 2780 Planarity : 0.004 0.046 3156 Dihedral : 11.827 179.926 2560 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.25 % Rotamer: Outliers : 2.26 % Allowed : 22.94 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.07 (0.18), residues: 2216 helix: 0.51 (0.18), residues: 880 sheet: 0.44 (0.25), residues: 416 loop : -0.72 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.002 0.001 HIS D 480 PHE 0.007 0.001 PHE A 162 TYR 0.012 0.001 TYR B 42 ARG 0.005 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 2.328 Fit side-chains REVERT: A 57 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: A 156 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7350 (tpt) REVERT: A 379 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5974 (tp30) REVERT: A 550 ARG cc_start: 0.7208 (mmt-90) cc_final: 0.6961 (mmp80) REVERT: B 156 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7356 (tpt) REVERT: B 379 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5876 (tt0) REVERT: B 448 MET cc_start: 0.7672 (mtm) cc_final: 0.7390 (mtt) REVERT: B 550 ARG cc_start: 0.7214 (mmt-90) cc_final: 0.6926 (mmp80) REVERT: C 57 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: C 379 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5939 (tp30) REVERT: D 57 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: D 156 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7409 (tpt) REVERT: D 379 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6030 (tp30) REVERT: D 448 MET cc_start: 0.7772 (mtt) cc_final: 0.7553 (mtt) REVERT: D 550 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.6876 (mmp80) outliers start: 44 outliers final: 21 residues processed: 262 average time/residue: 1.3429 time to fit residues: 392.5915 Evaluate side-chains 248 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 0.0570 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 192 optimal weight: 0.0970 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 480 HIS C 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18316 Z= 0.147 Angle : 0.593 7.043 24876 Z= 0.281 Chirality : 0.044 0.125 2780 Planarity : 0.004 0.045 3156 Dihedral : 11.643 176.577 2560 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 2.11 % Allowed : 22.99 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.00 (0.18), residues: 2216 helix: 0.56 (0.18), residues: 880 sheet: 0.45 (0.24), residues: 416 loop : -0.66 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 358 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE D 162 TYR 0.012 0.001 TYR B 42 ARG 0.005 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 1.970 Fit side-chains REVERT: A 57 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: A 379 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6017 (tp30) REVERT: A 550 ARG cc_start: 0.7174 (mmt-90) cc_final: 0.6922 (mmp80) REVERT: B 448 MET cc_start: 0.7653 (mtm) cc_final: 0.7335 (mtt) REVERT: B 550 ARG cc_start: 0.7200 (mmt-90) cc_final: 0.6910 (mmp80) REVERT: C 379 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5907 (tp30) REVERT: D 156 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7407 (tpt) REVERT: D 379 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5980 (tp30) REVERT: D 550 ARG cc_start: 0.7147 (mmt-90) cc_final: 0.6863 (mmp80) outliers start: 41 outliers final: 21 residues processed: 266 average time/residue: 1.3803 time to fit residues: 410.5731 Evaluate side-chains 252 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.9980 chunk 185 optimal weight: 0.0980 chunk 197 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 178 optimal weight: 0.0870 chunk 186 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18316 Z= 0.182 Angle : 0.618 6.550 24876 Z= 0.296 Chirality : 0.045 0.125 2780 Planarity : 0.005 0.046 3156 Dihedral : 11.706 174.606 2560 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 1.95 % Allowed : 23.25 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.04 (0.18), residues: 2216 helix: 0.55 (0.18), residues: 880 sheet: 0.52 (0.25), residues: 408 loop : -0.62 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 358 HIS 0.005 0.001 HIS A 116 PHE 0.012 0.001 PHE A 162 TYR 0.012 0.001 TYR D 106 ARG 0.006 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 2.238 Fit side-chains REVERT: A 57 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6365 (tm-30) REVERT: A 379 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6042 (tp30) REVERT: A 550 ARG cc_start: 0.7189 (mmt-90) cc_final: 0.6929 (mmp80) REVERT: B 57 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6500 (tm-30) REVERT: B 171 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6247 (ppp-140) REVERT: B 448 MET cc_start: 0.7657 (mtm) cc_final: 0.7399 (mtt) REVERT: B 550 ARG cc_start: 0.7195 (mmt-90) cc_final: 0.6894 (mmp80) REVERT: C 57 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: C 379 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5894 (tp30) REVERT: C 535 LYS cc_start: 0.7680 (tttt) cc_final: 0.7201 (mtpt) REVERT: D 156 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7405 (tpt) REVERT: D 411 ARG cc_start: 0.6489 (ptp-170) cc_final: 0.6255 (ptp-170) REVERT: D 550 ARG cc_start: 0.7190 (mmt-90) cc_final: 0.6873 (mmp80) outliers start: 38 outliers final: 22 residues processed: 263 average time/residue: 1.3503 time to fit residues: 396.6198 Evaluate side-chains 253 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.7980 chunk 127 optimal weight: 0.0170 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 134 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18316 Z= 0.173 Angle : 0.612 6.417 24876 Z= 0.292 Chirality : 0.045 0.124 2780 Planarity : 0.004 0.045 3156 Dihedral : 11.679 174.474 2560 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 1.95 % Allowed : 23.41 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.04 (0.18), residues: 2216 helix: 0.55 (0.18), residues: 880 sheet: 0.46 (0.24), residues: 416 loop : -0.58 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 358 HIS 0.004 0.001 HIS A 116 PHE 0.011 0.001 PHE D 162 TYR 0.011 0.001 TYR A 106 ARG 0.007 0.000 ARG A 411 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 2.246 Fit side-chains REVERT: A 57 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: A 379 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6042 (tp30) REVERT: A 550 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.6897 (mmp80) REVERT: B 57 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: B 171 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6173 (ppp-140) REVERT: B 448 MET cc_start: 0.7655 (mtm) cc_final: 0.7421 (mtt) REVERT: B 550 ARG cc_start: 0.7189 (mmt-90) cc_final: 0.6886 (mmp80) REVERT: C 57 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: C 171 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6241 (ppp-140) REVERT: C 535 LYS cc_start: 0.7661 (tttt) cc_final: 0.7197 (mtpt) REVERT: D 156 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7410 (tpt) REVERT: D 550 ARG cc_start: 0.7155 (mmt-90) cc_final: 0.6861 (mmp80) outliers start: 38 outliers final: 23 residues processed: 259 average time/residue: 1.4324 time to fit residues: 414.4147 Evaluate side-chains 252 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129692 restraints weight = 18396.246| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.47 r_work: 0.3350 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18316 Z= 0.174 Angle : 0.613 6.434 24876 Z= 0.293 Chirality : 0.045 0.124 2780 Planarity : 0.004 0.045 3156 Dihedral : 11.657 173.930 2560 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.90 % Allowed : 23.66 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.05 (0.18), residues: 2216 helix: 0.52 (0.18), residues: 880 sheet: 0.55 (0.25), residues: 408 loop : -0.58 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 358 HIS 0.004 0.001 HIS B 116 PHE 0.011 0.001 PHE D 162 TYR 0.011 0.001 TYR C 106 ARG 0.007 0.000 ARG A 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7101.87 seconds wall clock time: 126 minutes 52.06 seconds (7612.06 seconds total)