Starting phenix.real_space_refine on Mon Feb 19 18:41:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/02_2024/8f1c_28793_trim_updated.pdb" } resolution = 2.92 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= 0.011 sd= 0.045 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: 9 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 Cl 4 4.86 5 C 8520 2.51 5 N 2120 2.21 5 O 2208 1.98 5 H 12184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25116 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6194 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6194 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6194 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6194 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {' K': 4, ' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1518 SG CYS A 104 63.879 52.710 75.558 1.00 53.86 S ATOM 19787 SG CYS D 83 65.005 56.491 77.460 1.00 61.77 S ATOM 1205 SG CYS A 83 77.914 65.005 77.454 1.00 61.77 S ATOM 7712 SG CYS B 104 81.683 63.875 75.562 1.00 53.86 S ATOM 7399 SG CYS B 83 69.393 77.914 77.459 1.00 61.77 S ATOM 13906 SG CYS C 104 70.526 81.685 75.562 1.00 53.86 S ATOM 13593 SG CYS C 83 56.488 69.394 77.460 1.00 61.77 S ATOM 20100 SG CYS D 104 52.714 70.529 75.561 1.00 53.86 S Time building chain proxies: 11.50, per 1000 atoms: 0.46 Number of scatterers: 25116 At special positions: 0 Unit cell: (135.24, 135.24, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 4 29.99 K 4 19.00 Cl 4 17.00 S 68 16.00 P 4 15.00 O 2208 8.00 N 2120 7.00 C 8520 6.00 H 12184 1.00 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=0, symmetry=0 Time building additional restraints: 19.74 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 601 " - pdb=" SG CYS D 83 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS B 83 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 104 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS C 83 " 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 60.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.883A pdb=" N ALA A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 106 through 109 No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 189 through 211 removed outlier: 3.914A pdb=" N THR A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 265 removed outlier: 3.620A pdb=" N GLU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 279 through 293 removed outlier: 3.698A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 300 through 317 removed outlier: 4.456A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.581A pdb=" N THR A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 342 through 368 removed outlier: 4.127A pdb=" N ARG A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.606A pdb=" N MET A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 451 Proline residue: A 431 - end of helix removed outlier: 4.912A pdb=" N VAL A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 61 through 73 removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 106 through 109 No H-bonds generated for 'chain 'B' and resid 106 through 109' Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 189 through 211 removed outlier: 3.913A pdb=" N THR B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 removed outlier: 3.619A pdb=" N GLU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 279 through 293 removed outlier: 3.698A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Proline residue: B 288 - end of helix Processing helix chain 'B' and resid 300 through 317 removed outlier: 4.456A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 325 removed outlier: 3.582A pdb=" N THR B 325 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 342 through 368 removed outlier: 4.128A pdb=" N ARG B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 398 removed outlier: 3.606A pdb=" N MET B 398 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 451 Proline residue: B 431 - end of helix removed outlier: 4.913A pdb=" N VAL B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.883A pdb=" N ALA C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 106 through 109 No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 189 through 211 removed outlier: 3.913A pdb=" N THR C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 265 removed outlier: 3.619A pdb=" N GLU C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 279 through 293 removed outlier: 3.698A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 300 through 317 removed outlier: 4.456A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 3.581A pdb=" N THR C 325 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 342 through 368 removed outlier: 4.129A pdb=" N ARG C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 398 removed outlier: 3.606A pdb=" N MET C 398 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 451 Proline residue: C 431 - end of helix removed outlier: 4.912A pdb=" N VAL C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.882A pdb=" N ALA D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 106 through 109 No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 189 through 211 removed outlier: 3.913A pdb=" N THR D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 265 removed outlier: 3.619A pdb=" N GLU D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 279 through 293 removed outlier: 3.698A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Proline residue: D 288 - end of helix Processing helix chain 'D' and resid 300 through 317 removed outlier: 4.456A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 325 removed outlier: 3.582A pdb=" N THR D 325 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 342 through 368 removed outlier: 4.128A pdb=" N ARG D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 398 removed outlier: 3.606A pdb=" N MET D 398 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 451 Proline residue: D 431 - end of helix removed outlier: 4.912A pdb=" N VAL D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR A 21 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 10 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE A 55 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR B 21 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 10 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE B 55 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 10 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE C 55 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR D 21 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 10 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE D 55 " --> pdb=" O ASN D 13 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1656 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: 8.54 Time building geometry restraints manager: 20.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12160 1.03 - 1.23: 36 1.23 - 1.42: 5800 1.42 - 1.61: 7400 1.61 - 1.81: 108 Bond restraints: 25504 Sorted by residual: bond pdb=" C14 X9T A 602 " pdb=" O18 X9T A 602 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C14 X9T D 602 " pdb=" O18 X9T D 602 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C14 X9T C 602 " pdb=" O18 X9T C 602 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C14 X9T B 602 " pdb=" O18 X9T B 602 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C23 X9T D 602 " pdb=" N29 X9T D 602 " ideal model delta sigma weight residual 1.482 1.384 0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 25499 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.42: 291 105.42 - 112.58: 28066 112.58 - 119.74: 7077 119.74 - 126.89: 10045 126.89 - 134.05: 265 Bond angle restraints: 45744 Sorted by residual: angle pdb=" C1 X9T C 602 " pdb=" C2 X9T C 602 " pdb=" C7 X9T C 602 " ideal model delta sigma weight residual 105.54 119.61 -14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C1 X9T A 602 " pdb=" C2 X9T A 602 " pdb=" C7 X9T A 602 " ideal model delta sigma weight residual 105.54 119.61 -14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C1 X9T D 602 " pdb=" C2 X9T D 602 " pdb=" C7 X9T D 602 " ideal model delta sigma weight residual 105.54 119.61 -14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C1 X9T B 602 " pdb=" C2 X9T B 602 " pdb=" C7 X9T B 602 " ideal model delta sigma weight residual 105.54 119.59 -14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C28 X9T B 602 " pdb=" C26 X9T B 602 " pdb=" N27 X9T B 602 " ideal model delta sigma weight residual 130.21 117.12 13.09 3.00e+00 1.11e-01 1.90e+01 ... (remaining 45739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 11163 16.07 - 32.13: 697 32.13 - 48.20: 168 48.20 - 64.27: 92 64.27 - 80.33: 20 Dihedral angle restraints: 12140 sinusoidal: 6340 harmonic: 5800 Sorted by residual: dihedral pdb=" CA ILE A 318 " pdb=" CB ILE A 318 " pdb=" CG1 ILE A 318 " pdb=" CD1 ILE A 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.72 46.28 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" CA ILE D 318 " pdb=" CB ILE D 318 " pdb=" CG1 ILE D 318 " pdb=" CD1 ILE D 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.74 46.26 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" CA ILE B 318 " pdb=" CB ILE B 318 " pdb=" CG1 ILE B 318 " pdb=" CD1 ILE B 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.74 46.26 3 1.50e+01 4.44e-03 8.31e+00 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1135 0.024 - 0.049: 502 0.049 - 0.073: 192 0.073 - 0.097: 90 0.097 - 0.121: 41 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA ILE D 12 " pdb=" N ILE D 12 " pdb=" C ILE D 12 " pdb=" CB ILE D 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE B 12 " pdb=" N ILE B 12 " pdb=" C ILE B 12 " pdb=" CB ILE B 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1957 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 102 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 103 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 102 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 103 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 102 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 103 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 103 " -0.020 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.36: 8160 2.36 - 3.06: 68517 3.06 - 3.75: 85487 3.75 - 4.45: 133121 4.45 - 5.14: 203975 Nonbonded interactions: 499260 Sorted by model distance: nonbonded pdb=" OD2 ASP A 100 " pdb=" HZ1 LYS D 458 " model vdw 1.667 1.850 nonbonded pdb=" HZ1 LYS A 458 " pdb=" OD2 ASP B 100 " model vdw 1.668 1.850 nonbonded pdb=" HZ1 LYS B 458 " pdb=" OD2 ASP C 100 " model vdw 1.672 1.850 nonbonded pdb=" HZ1 LYS C 458 " pdb=" OD2 ASP D 100 " model vdw 1.673 1.850 nonbonded pdb=" O GLU B 210 " pdb="HD21 ASN B 216 " model vdw 1.693 1.850 ... (remaining 499255 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 7 through 463 or resid 601 through 603)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.170 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: 0.340 Extract box with map and model: 6.230 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 88.790 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.005 0.120 13320 Z= 0.331 Angle : 0.720 14.074 18136 Z= 0.296 Chirality : 0.036 0.121 1960 Planarity : 0.004 0.035 2252 Dihedral : 11.355 80.333 4708 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.61 % Allowed : 3.36 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.22), residues: 1552 helix: 1.68 (0.18), residues: 908 sheet: -2.91 (0.85), residues: 40 loop : -0.95 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 255 HIS 0.001 0.000 HIS A 60 PHE 0.006 0.001 PHE C 328 TYR 0.005 0.001 TYR C 71 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 1.944 Fit side-chains REVERT: A 412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7712 (p) REVERT: A 447 MET cc_start: 0.8507 (mmm) cc_final: 0.8121 (mmt) REVERT: B 412 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 447 MET cc_start: 0.8497 (mmm) cc_final: 0.8107 (mmt) REVERT: C 412 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.7690 (p) REVERT: C 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8109 (mmt) REVERT: D 412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7681 (p) REVERT: D 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8112 (mmt) outliers start: 8 outliers final: 0 residues processed: 213 average time/residue: 2.3724 time to fit residues: 555.7309 Evaluate side-chains 145 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 372 GLN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13320 Z= 0.301 Angle : 0.552 6.846 18136 Z= 0.277 Chirality : 0.040 0.142 1960 Planarity : 0.005 0.044 2252 Dihedral : 9.460 85.514 1920 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.15 % Allowed : 9.40 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.22), residues: 1552 helix: 1.41 (0.17), residues: 908 sheet: -2.43 (0.85), residues: 40 loop : -1.21 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 392 HIS 0.003 0.001 HIS A 60 PHE 0.015 0.001 PHE A 384 TYR 0.008 0.001 TYR D 365 ARG 0.002 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.977 Fit side-chains REVERT: A 172 TRP cc_start: 0.6910 (m100) cc_final: 0.6700 (m100) REVERT: A 412 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 23 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7729 (ttm-80) REVERT: B 324 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 412 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8472 (p) REVERT: C 324 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8033 (mp) REVERT: C 412 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 324 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8030 (mp) REVERT: D 412 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8473 (p) outliers start: 15 outliers final: 3 residues processed: 151 average time/residue: 1.8909 time to fit residues: 321.9472 Evaluate side-chains 140 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN D 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13320 Z= 0.250 Angle : 0.507 5.552 18136 Z= 0.252 Chirality : 0.039 0.133 1960 Planarity : 0.005 0.043 2252 Dihedral : 9.170 83.647 1920 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.83 % Allowed : 9.10 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1552 helix: 1.45 (0.18), residues: 904 sheet: -2.55 (0.81), residues: 40 loop : -1.24 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS C 60 PHE 0.017 0.001 PHE B 56 TYR 0.007 0.001 TYR D 365 ARG 0.001 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 2.140 Fit side-chains REVERT: A 412 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 412 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8448 (p) REVERT: C 412 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8448 (p) REVERT: D 412 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8449 (p) outliers start: 24 outliers final: 4 residues processed: 145 average time/residue: 1.9474 time to fit residues: 317.7969 Evaluate side-chains 136 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8260 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13320 Z= 0.214 Angle : 0.488 5.512 18136 Z= 0.243 Chirality : 0.038 0.129 1960 Planarity : 0.005 0.043 2252 Dihedral : 8.390 63.490 1920 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.22 % Allowed : 9.63 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.22), residues: 1552 helix: 1.36 (0.18), residues: 948 sheet: -2.60 (0.79), residues: 40 loop : -1.32 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 255 HIS 0.002 0.000 HIS C 60 PHE 0.014 0.001 PHE A 384 TYR 0.007 0.001 TYR D 365 ARG 0.001 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 2.104 Fit side-chains REVERT: A 10 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7556 (tp) REVERT: A 447 MET cc_start: 0.8746 (mmm) cc_final: 0.8362 (mmt) REVERT: B 10 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7586 (tp) REVERT: B 447 MET cc_start: 0.8735 (mmm) cc_final: 0.8343 (mmt) REVERT: C 447 MET cc_start: 0.8737 (mmm) cc_final: 0.8345 (mmt) REVERT: D 10 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7585 (tp) REVERT: D 447 MET cc_start: 0.8737 (mmm) cc_final: 0.8346 (mmt) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 1.9615 time to fit residues: 317.9311 Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13320 Z= 0.317 Angle : 0.550 6.386 18136 Z= 0.275 Chirality : 0.041 0.139 1960 Planarity : 0.005 0.046 2252 Dihedral : 8.230 64.040 1916 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.53 % Allowed : 10.02 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.22), residues: 1552 helix: 1.21 (0.18), residues: 932 sheet: -2.66 (0.76), residues: 40 loop : -1.39 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.003 0.001 HIS D 60 PHE 0.018 0.001 PHE D 384 TYR 0.009 0.001 TYR C 365 ARG 0.002 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 2.093 Fit side-chains REVERT: A 10 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7470 (tp) REVERT: A 412 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 10 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7488 (tp) REVERT: B 412 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8515 (p) REVERT: C 10 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7447 (tp) REVERT: C 412 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8535 (p) REVERT: D 10 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7480 (tp) REVERT: D 412 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8520 (p) outliers start: 20 outliers final: 12 residues processed: 151 average time/residue: 1.8464 time to fit residues: 314.9780 Evaluate side-chains 151 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.8271 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13320 Z= 0.243 Angle : 0.512 5.362 18136 Z= 0.255 Chirality : 0.039 0.128 1960 Planarity : 0.005 0.044 2252 Dihedral : 7.815 63.227 1916 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.53 % Allowed : 11.01 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.22), residues: 1552 helix: 1.28 (0.18), residues: 940 sheet: -2.57 (0.77), residues: 40 loop : -1.38 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.002 0.000 HIS D 60 PHE 0.016 0.001 PHE B 384 TYR 0.008 0.001 TYR C 365 ARG 0.001 0.000 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 2.122 Fit side-chains REVERT: A 412 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 412 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 10 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7431 (tp) REVERT: C 412 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8439 (p) REVERT: D 412 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8429 (p) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 1.9078 time to fit residues: 327.2331 Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- 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: 0.8257 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13320 Z= 0.200 Angle : 0.495 5.115 18136 Z= 0.244 Chirality : 0.038 0.126 1960 Planarity : 0.005 0.043 2252 Dihedral : 7.619 62.962 1916 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.53 % Allowed : 11.31 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.22), residues: 1552 helix: 1.35 (0.18), residues: 948 sheet: -2.45 (0.78), residues: 40 loop : -1.28 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.002 0.000 HIS C 60 PHE 0.014 0.001 PHE D 384 TYR 0.006 0.001 TYR D 365 ARG 0.001 0.000 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.845 Fit side-chains REVERT: A 10 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7478 (tp) REVERT: A 412 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 10 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7461 (tp) REVERT: B 412 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8424 (p) REVERT: C 10 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7430 (tp) REVERT: C 412 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 10 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7465 (tp) REVERT: D 412 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8431 (p) outliers start: 20 outliers final: 12 residues processed: 155 average time/residue: 1.8488 time to fit residues: 324.4212 Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8281 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13320 Z= 0.294 Angle : 0.541 6.111 18136 Z= 0.269 Chirality : 0.040 0.135 1960 Planarity : 0.005 0.045 2252 Dihedral : 8.059 63.660 1916 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.53 % Allowed : 11.16 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.22), residues: 1552 helix: 1.22 (0.17), residues: 952 sheet: -2.28 (0.78), residues: 40 loop : -1.37 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.003 0.001 HIS C 60 PHE 0.018 0.001 PHE B 384 TYR 0.009 0.001 TYR B 365 ARG 0.001 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.980 Fit side-chains REVERT: A 10 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7506 (tp) REVERT: A 412 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 10 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7496 (tp) REVERT: B 412 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 412 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8523 (p) REVERT: D 10 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7509 (tp) REVERT: D 412 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8509 (p) outliers start: 20 outliers final: 12 residues processed: 151 average time/residue: 1.8884 time to fit residues: 322.0356 Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13320 Z= 0.310 Angle : 0.552 6.001 18136 Z= 0.275 Chirality : 0.041 0.167 1960 Planarity : 0.005 0.045 2252 Dihedral : 8.245 63.458 1916 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.53 % Allowed : 11.47 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.22), residues: 1552 helix: 1.21 (0.17), residues: 940 sheet: -2.13 (0.78), residues: 40 loop : -1.48 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS A 60 PHE 0.018 0.001 PHE C 384 TYR 0.009 0.001 TYR D 365 ARG 0.001 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.882 Fit side-chains REVERT: A 10 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7547 (tp) REVERT: A 412 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 10 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7564 (tp) REVERT: B 412 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8514 (p) REVERT: C 412 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8516 (p) REVERT: D 10 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7574 (tp) REVERT: D 412 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8520 (p) outliers start: 20 outliers final: 12 residues processed: 146 average time/residue: 1.9243 time to fit residues: 315.8434 Evaluate side-chains 143 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8255 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13320 Z= 0.197 Angle : 0.496 4.982 18136 Z= 0.244 Chirality : 0.038 0.143 1960 Planarity : 0.005 0.043 2252 Dihedral : 7.848 62.732 1916 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.53 % Allowed : 11.77 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.22), residues: 1552 helix: 1.38 (0.18), residues: 940 sheet: -1.93 (0.80), residues: 40 loop : -1.36 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.002 0.000 HIS A 60 PHE 0.013 0.001 PHE D 384 TYR 0.006 0.001 TYR C 365 ARG 0.003 0.000 ARG B 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 2.191 Fit side-chains REVERT: A 412 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 412 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8409 (p) REVERT: C 412 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8411 (p) REVERT: C 447 MET cc_start: 0.8715 (mmm) cc_final: 0.8359 (mmt) REVERT: D 412 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8379 (p) REVERT: D 447 MET cc_start: 0.8716 (mmm) cc_final: 0.8360 (mmt) outliers start: 20 outliers final: 12 residues processed: 143 average time/residue: 2.0203 time to fit residues: 326.4768 Evaluate side-chains 140 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 0.0670 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144529 restraints weight = 37333.720| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.37 r_work: 0.3342 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13320 Z= 0.195 Angle : 0.498 4.949 18136 Z= 0.245 Chirality : 0.038 0.135 1960 Planarity : 0.004 0.043 2252 Dihedral : 7.775 62.842 1916 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.22 % Allowed : 12.16 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.22), residues: 1552 helix: 1.40 (0.18), residues: 940 sheet: -1.68 (0.80), residues: 40 loop : -1.33 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.002 0.000 HIS A 60 PHE 0.014 0.001 PHE A 194 TYR 0.006 0.001 TYR C 365 ARG 0.002 0.000 ARG B 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6961.95 seconds wall clock time: 123 minutes 19.26 seconds (7399.26 seconds total)