Starting phenix.real_space_refine on Wed Feb 14 21:49:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/02_2024/7nsg_12566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/02_2024/7nsg_12566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/02_2024/7nsg_12566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/02_2024/7nsg_12566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/02_2024/7nsg_12566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/02_2024/7nsg_12566.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 69 5.16 5 C 6855 2.51 5 N 1575 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 351": "OD1" <-> "OD2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 351": "OD1" <-> "OD2" Residue "C ASP 386": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10356 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3255 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3255 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3255 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 197 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR5': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR8': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 171 Chain: "B" Number of atoms: 197 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR5': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR8': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 171 Chain: "C" Number of atoms: 197 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR5': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR8': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 171 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AUR5 A 501 " occ=0.50 ... (10 atoms not shown) pdb=" O3 AUR5 A 501 " occ=0.50 residue: pdb=" N BUR8 A 502 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BUR8 A 502 " occ=0.50 residue: pdb=" N AUR5 B 501 " occ=0.50 ... (10 atoms not shown) pdb=" O3 AUR5 B 501 " occ=0.50 residue: pdb=" N BUR8 B 502 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BUR8 B 502 " occ=0.50 residue: pdb=" N AUR5 C 501 " occ=0.50 ... (10 atoms not shown) pdb=" O3 AUR5 C 501 " occ=0.50 residue: pdb=" N BUR8 C 502 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BUR8 C 502 " occ=0.50 Time building chain proxies: 6.31, per 1000 atoms: 0.61 Number of scatterers: 10356 At special positions: 0 Unit cell: (116.202, 116.202, 89.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 9 15.00 O 1848 8.00 N 1575 7.00 C 6855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 81.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 18 through 40 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.566A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.621A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.513A pdb=" N ARG A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 4.230A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.504A pdb=" N LEU A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.814A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.865A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.765A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.307A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.653A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.627A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.092A pdb=" N ALA A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 409 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.542A pdb=" N LEU A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.801A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.843A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.616A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 18 through 40 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.566A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.621A pdb=" N ILE B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.514A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 4.230A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.505A pdb=" N LEU B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.814A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.866A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.766A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.306A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.654A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.627A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.091A pdb=" N ALA B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 409 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.541A pdb=" N LEU B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.801A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.844A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.616A pdb=" N GLU B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 18 through 40 Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.566A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 3.621A pdb=" N ILE C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.514A pdb=" N ARG C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 150 removed outlier: 4.230A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.504A pdb=" N LEU C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.814A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.866A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.766A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.307A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.654A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.627A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.092A pdb=" N ALA C 408 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 409 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.542A pdb=" N LEU C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.801A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.845A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 476 removed outlier: 3.615A pdb=" N GLU C 471 " --> pdb=" O LYS C 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 168 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 168 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 168 708 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1623 1.32 - 1.44: 2352 1.44 - 1.56: 6381 1.56 - 1.68: 18 1.68 - 1.80: 123 Bond restraints: 10497 Sorted by residual: bond pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 1.205 1.340 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C21 PC1 A 506 " pdb=" O22 PC1 A 506 " ideal model delta sigma weight residual 1.205 1.340 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C21 PC1 C 506 " pdb=" O22 PC1 C 506 " ideal model delta sigma weight residual 1.205 1.339 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C21 PC1 A 506 " pdb=" O21 PC1 A 506 " ideal model delta sigma weight residual 1.331 1.200 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C21 PC1 C 506 " pdb=" O21 PC1 C 506 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.00e-02 2.50e+03 4.25e+01 ... (remaining 10492 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.88: 252 105.88 - 112.90: 5826 112.90 - 119.91: 3874 119.91 - 126.93: 4162 126.93 - 133.94: 61 Bond angle restraints: 14175 Sorted by residual: angle pdb=" N ILE A 391 " pdb=" CA ILE A 391 " pdb=" C ILE A 391 " ideal model delta sigma weight residual 112.90 106.66 6.24 9.60e-01 1.09e+00 4.23e+01 angle pdb=" N ILE B 391 " pdb=" CA ILE B 391 " pdb=" C ILE B 391 " ideal model delta sigma weight residual 112.90 106.67 6.23 9.60e-01 1.09e+00 4.21e+01 angle pdb=" N ILE C 391 " pdb=" CA ILE C 391 " pdb=" C ILE C 391 " ideal model delta sigma weight residual 112.90 106.67 6.23 9.60e-01 1.09e+00 4.20e+01 angle pdb=" C22 PC1 A 506 " pdb=" C21 PC1 A 506 " pdb=" O22 PC1 A 506 " ideal model delta sigma weight residual 125.37 111.22 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C22 PC1 B 506 " pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 125.37 111.28 14.09 3.00e+00 1.11e-01 2.21e+01 ... (remaining 14170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5981 17.90 - 35.79: 547 35.79 - 53.69: 93 53.69 - 71.58: 24 71.58 - 89.48: 9 Dihedral angle restraints: 6654 sinusoidal: 2949 harmonic: 3705 Sorted by residual: dihedral pdb=" CA GLU B 48 " pdb=" C GLU B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLU A 48 " pdb=" C GLU A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1226 0.048 - 0.095: 406 0.095 - 0.143: 104 0.143 - 0.190: 25 0.190 - 0.238: 6 Chirality restraints: 1767 Sorted by residual: chirality pdb=" C1 BUR8 C 502 " pdb=" C2 BUR8 C 502 " pdb=" C4 BUR8 C 502 " pdb=" O1 BUR8 C 502 " both_signs ideal model delta sigma weight residual False 2.69 2.93 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 BUR8 B 502 " pdb=" C2 BUR8 B 502 " pdb=" C4 BUR8 B 502 " pdb=" O1 BUR8 B 502 " both_signs ideal model delta sigma weight residual False 2.69 2.93 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 BUR8 A 502 " pdb=" C2 BUR8 A 502 " pdb=" C4 BUR8 A 502 " pdb=" O1 BUR8 A 502 " both_signs ideal model delta sigma weight residual False 2.69 2.93 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1764 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO C 302 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.037 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO B 302 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.037 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 302 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.031 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2968 2.83 - 3.34: 9327 3.34 - 3.86: 15903 3.86 - 4.38: 18601 4.38 - 4.90: 33103 Nonbonded interactions: 79902 Sorted by model distance: nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.307 2.440 nonbonded pdb=" O SER B 331 " pdb=" OG SER B 331 " model vdw 2.307 2.440 nonbonded pdb=" O SER C 331 " pdb=" OG SER C 331 " model vdw 2.308 2.440 nonbonded pdb=" OD1 ASP A 444 " pdb=" N1 AUR5 A 501 " model vdw 2.405 2.520 nonbonded pdb=" OD1 ASP B 444 " pdb=" N1 AUR5 B 501 " model vdw 2.411 2.520 ... (remaining 79897 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 10 through 476 or resid 503 through 507)) selection = (chain 'B' and (resid 10 through 476 or resid 503 through 507)) selection = (chain 'C' and (resid 10 through 476 or resid 503 through 507)) } 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=0.50 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.390 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.540 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 10497 Z= 0.594 Angle : 1.005 14.147 14175 Z= 0.521 Chirality : 0.052 0.238 1767 Planarity : 0.007 0.055 1677 Dihedral : 14.071 89.476 4260 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -3.82 (0.18), residues: 1272 helix: -2.30 (0.12), residues: 963 sheet: -1.29 (0.76), residues: 60 loop : -2.71 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 276 HIS 0.001 0.000 HIS B 296 PHE 0.035 0.003 PHE A 341 TYR 0.021 0.003 TYR C 373 ARG 0.003 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 4.190 Fit side-chains REVERT: A 165 LYS cc_start: 0.8204 (pttt) cc_final: 0.7673 (ptmm) REVERT: A 258 MET cc_start: 0.7869 (ttp) cc_final: 0.7593 (ttp) REVERT: A 325 LEU cc_start: 0.8155 (tp) cc_final: 0.7886 (tp) REVERT: A 353 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7518 (ttm110) REVERT: A 449 MET cc_start: 0.7640 (ttp) cc_final: 0.7254 (ttt) REVERT: A 473 MET cc_start: 0.7086 (mtm) cc_final: 0.6473 (tmm) REVERT: B 39 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.7097 (ttt180) REVERT: B 165 LYS cc_start: 0.8204 (pttt) cc_final: 0.7613 (ptmm) REVERT: B 258 MET cc_start: 0.7822 (ttp) cc_final: 0.7547 (ttt) REVERT: B 353 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7532 (ttm110) REVERT: B 419 MET cc_start: 0.8770 (tpt) cc_final: 0.8229 (tpt) REVERT: B 449 MET cc_start: 0.7654 (ttp) cc_final: 0.7317 (ttt) REVERT: C 165 LYS cc_start: 0.8169 (pttt) cc_final: 0.7572 (ptmm) REVERT: C 248 MET cc_start: 0.8461 (mmm) cc_final: 0.8240 (mmm) REVERT: C 258 MET cc_start: 0.7831 (ttp) cc_final: 0.7486 (ttp) REVERT: C 315 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6752 (mmm160) REVERT: C 353 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7258 (ttm110) REVERT: C 419 MET cc_start: 0.8659 (tpt) cc_final: 0.8020 (tpt) REVERT: C 449 MET cc_start: 0.7530 (ttp) cc_final: 0.7198 (ttt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2837 time to fit residues: 65.8175 Evaluate side-chains 134 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 413 GLN C 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10497 Z= 0.186 Angle : 0.526 8.586 14175 Z= 0.275 Chirality : 0.038 0.141 1767 Planarity : 0.004 0.037 1677 Dihedral : 10.153 81.003 2064 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.13 % Allowed : 7.55 % Favored : 91.31 % 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: -0.95 (0.23), residues: 1272 helix: -0.01 (0.17), residues: 969 sheet: -1.00 (0.76), residues: 60 loop : -2.63 (0.32), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 441 HIS 0.000 0.000 HIS A 296 PHE 0.017 0.002 PHE A 341 TYR 0.011 0.001 TYR A 373 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.023 Fit side-chains REVERT: A 165 LYS cc_start: 0.8170 (pttt) cc_final: 0.7659 (ptmm) REVERT: A 258 MET cc_start: 0.7803 (ttp) cc_final: 0.7464 (ttt) REVERT: A 353 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7631 (ttm110) REVERT: A 388 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6828 (p0) REVERT: A 449 MET cc_start: 0.7641 (ttp) cc_final: 0.7345 (ttt) REVERT: B 165 LYS cc_start: 0.8188 (pttt) cc_final: 0.7593 (ptmm) REVERT: B 258 MET cc_start: 0.7792 (ttp) cc_final: 0.7543 (ttt) REVERT: B 449 MET cc_start: 0.7613 (ttp) cc_final: 0.7349 (ttp) REVERT: C 165 LYS cc_start: 0.8139 (pttt) cc_final: 0.7575 (ptmm) REVERT: C 258 MET cc_start: 0.7925 (ttp) cc_final: 0.7583 (ttt) REVERT: C 315 ARG cc_start: 0.7196 (mmt90) cc_final: 0.6762 (mmm160) REVERT: C 353 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7362 (ttm110) REVERT: C 356 ARG cc_start: 0.7694 (mmt-90) cc_final: 0.7406 (mtt-85) outliers start: 12 outliers final: 8 residues processed: 152 average time/residue: 0.2679 time to fit residues: 55.4781 Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 0.0270 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10497 Z= 0.132 Angle : 0.475 8.053 14175 Z= 0.243 Chirality : 0.037 0.124 1767 Planarity : 0.003 0.030 1677 Dihedral : 9.175 76.325 2064 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.51 % Allowed : 10.86 % Favored : 87.63 % 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: 0.38 (0.25), residues: 1272 helix: 1.03 (0.18), residues: 936 sheet: -0.72 (0.74), residues: 60 loop : -2.14 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 19 HIS 0.000 0.000 HIS A 296 PHE 0.010 0.001 PHE A 357 TYR 0.011 0.001 TYR A 373 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.109 Fit side-chains REVERT: A 165 LYS cc_start: 0.8106 (pttt) cc_final: 0.7610 (ptmm) REVERT: A 255 MET cc_start: 0.8733 (mmm) cc_final: 0.8519 (mmm) REVERT: A 258 MET cc_start: 0.7755 (ttp) cc_final: 0.7387 (ttt) REVERT: A 353 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7581 (ttm110) REVERT: A 449 MET cc_start: 0.7658 (ttp) cc_final: 0.7350 (ttt) REVERT: B 160 GLN cc_start: 0.8736 (pt0) cc_final: 0.8355 (pt0) REVERT: B 165 LYS cc_start: 0.8116 (pttt) cc_final: 0.7583 (ptmm) REVERT: B 258 MET cc_start: 0.7763 (ttp) cc_final: 0.7519 (ttt) REVERT: B 449 MET cc_start: 0.7521 (ttp) cc_final: 0.7192 (ttp) REVERT: C 165 LYS cc_start: 0.8093 (pttt) cc_final: 0.7571 (ptmm) REVERT: C 258 MET cc_start: 0.7822 (ttp) cc_final: 0.7477 (ttt) REVERT: C 353 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7319 (ttm110) REVERT: C 449 MET cc_start: 0.7634 (ttp) cc_final: 0.7237 (ttp) REVERT: C 473 MET cc_start: 0.6591 (mtm) cc_final: 0.6344 (mtm) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 0.2665 time to fit residues: 57.9908 Evaluate side-chains 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.0570 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7898 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10497 Z= 0.141 Angle : 0.478 9.709 14175 Z= 0.240 Chirality : 0.037 0.122 1767 Planarity : 0.003 0.028 1677 Dihedral : 8.822 71.257 2064 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.89 % Allowed : 11.33 % Favored : 86.78 % 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: 1.13 (0.25), residues: 1272 helix: 1.60 (0.18), residues: 918 sheet: -0.65 (0.74), residues: 60 loop : -1.66 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 19 HIS 0.000 0.000 HIS B 296 PHE 0.009 0.001 PHE C 159 TYR 0.008 0.001 TYR A 373 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.099 Fit side-chains REVERT: A 165 LYS cc_start: 0.8115 (pttt) cc_final: 0.7632 (ptmm) REVERT: A 258 MET cc_start: 0.7734 (ttp) cc_final: 0.7376 (ttt) REVERT: A 353 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7600 (ttm110) REVERT: A 449 MET cc_start: 0.7662 (ttp) cc_final: 0.7333 (ttt) REVERT: B 39 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7339 (mtp180) REVERT: B 160 GLN cc_start: 0.8723 (pt0) cc_final: 0.8351 (pt0) REVERT: B 165 LYS cc_start: 0.8119 (pttt) cc_final: 0.7583 (ptmm) REVERT: B 258 MET cc_start: 0.7804 (ttp) cc_final: 0.7487 (ttt) REVERT: B 449 MET cc_start: 0.7646 (ttp) cc_final: 0.7284 (ttp) REVERT: C 39 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7353 (mtp180) REVERT: C 165 LYS cc_start: 0.8097 (pttt) cc_final: 0.7570 (ptmm) REVERT: C 258 MET cc_start: 0.7817 (ttp) cc_final: 0.7472 (ttt) REVERT: C 449 MET cc_start: 0.7614 (ttp) cc_final: 0.7184 (ttp) outliers start: 20 outliers final: 12 residues processed: 157 average time/residue: 0.2608 time to fit residues: 55.1670 Evaluate side-chains 153 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10497 Z= 0.163 Angle : 0.480 8.106 14175 Z= 0.242 Chirality : 0.037 0.127 1767 Planarity : 0.003 0.027 1677 Dihedral : 8.788 69.418 2064 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.89 % Allowed : 11.90 % Favored : 86.21 % 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: 1.47 (0.25), residues: 1272 helix: 1.75 (0.18), residues: 936 sheet: -0.69 (0.73), residues: 60 loop : -1.30 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 19 HIS 0.000 0.000 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.008 0.001 TYR B 373 ARG 0.001 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.167 Fit side-chains REVERT: A 165 LYS cc_start: 0.8139 (pttt) cc_final: 0.7655 (ptmm) REVERT: A 258 MET cc_start: 0.7707 (ttp) cc_final: 0.7369 (ttt) REVERT: A 449 MET cc_start: 0.7683 (ttp) cc_final: 0.7349 (ttt) REVERT: B 39 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7432 (mtp180) REVERT: B 160 GLN cc_start: 0.8749 (pt0) cc_final: 0.8372 (pt0) REVERT: B 165 LYS cc_start: 0.8134 (pttt) cc_final: 0.7590 (ptmm) REVERT: B 258 MET cc_start: 0.7812 (ttp) cc_final: 0.7502 (ttt) REVERT: C 39 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7393 (mtp180) REVERT: C 165 LYS cc_start: 0.8113 (pttt) cc_final: 0.7584 (ptmm) REVERT: C 258 MET cc_start: 0.7755 (ttp) cc_final: 0.7406 (ttt) REVERT: C 315 ARG cc_start: 0.7092 (mpt-90) cc_final: 0.6771 (tpp-160) REVERT: C 449 MET cc_start: 0.7491 (ttp) cc_final: 0.7213 (ttt) outliers start: 20 outliers final: 15 residues processed: 158 average time/residue: 0.2790 time to fit residues: 60.3047 Evaluate side-chains 153 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10497 Z= 0.127 Angle : 0.461 8.395 14175 Z= 0.233 Chirality : 0.037 0.121 1767 Planarity : 0.003 0.026 1677 Dihedral : 8.543 66.814 2064 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.79 % Allowed : 12.46 % Favored : 85.74 % 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: 1.68 (0.25), residues: 1272 helix: 2.01 (0.18), residues: 921 sheet: -0.71 (0.73), residues: 60 loop : -1.46 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.000 0.000 HIS B 296 PHE 0.006 0.001 PHE A 159 TYR 0.007 0.001 TYR B 373 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.222 Fit side-chains REVERT: A 165 LYS cc_start: 0.8035 (pttt) cc_final: 0.7547 (ptmm) REVERT: A 258 MET cc_start: 0.7688 (ttp) cc_final: 0.7357 (ttt) REVERT: A 449 MET cc_start: 0.7693 (ttp) cc_final: 0.7385 (ttt) REVERT: B 39 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7363 (mtp180) REVERT: B 160 GLN cc_start: 0.8660 (pt0) cc_final: 0.8346 (pt0) REVERT: B 165 LYS cc_start: 0.8118 (pttt) cc_final: 0.7571 (ptmm) REVERT: B 258 MET cc_start: 0.7796 (ttp) cc_final: 0.7476 (ttt) REVERT: C 39 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7382 (mtp180) REVERT: C 165 LYS cc_start: 0.8100 (pttt) cc_final: 0.7573 (ptmm) REVERT: C 258 MET cc_start: 0.7729 (ttp) cc_final: 0.7404 (ttt) REVERT: C 315 ARG cc_start: 0.7036 (mpt-90) cc_final: 0.6784 (tpp-160) REVERT: C 449 MET cc_start: 0.7600 (ttp) cc_final: 0.7281 (ttp) outliers start: 19 outliers final: 10 residues processed: 154 average time/residue: 0.2463 time to fit residues: 52.6653 Evaluate side-chains 146 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10497 Z= 0.161 Angle : 0.478 7.770 14175 Z= 0.243 Chirality : 0.037 0.125 1767 Planarity : 0.003 0.026 1677 Dihedral : 8.568 65.877 2064 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.42 % Allowed : 12.84 % Favored : 85.74 % 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: 1.73 (0.25), residues: 1272 helix: 2.01 (0.18), residues: 924 sheet: -0.70 (0.74), residues: 60 loop : -1.36 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.000 0.000 HIS B 296 PHE 0.010 0.001 PHE A 240 TYR 0.007 0.001 TYR B 162 ARG 0.001 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.255 Fit side-chains REVERT: A 165 LYS cc_start: 0.8069 (pttt) cc_final: 0.7567 (ptmm) REVERT: A 258 MET cc_start: 0.7739 (ttp) cc_final: 0.7414 (ttt) REVERT: A 449 MET cc_start: 0.7684 (ttp) cc_final: 0.7336 (ttt) REVERT: B 39 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7440 (mtp180) REVERT: B 165 LYS cc_start: 0.8127 (pttt) cc_final: 0.7568 (ptmm) REVERT: B 258 MET cc_start: 0.7733 (ttp) cc_final: 0.7472 (ttt) REVERT: C 39 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7401 (mtp180) REVERT: C 165 LYS cc_start: 0.8104 (pttt) cc_final: 0.7584 (ptmm) REVERT: C 258 MET cc_start: 0.7780 (ttp) cc_final: 0.7431 (ttt) REVERT: C 315 ARG cc_start: 0.7055 (mpt-90) cc_final: 0.6791 (tpp-160) outliers start: 15 outliers final: 12 residues processed: 148 average time/residue: 0.2647 time to fit residues: 54.7726 Evaluate side-chains 146 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7911 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10497 Z= 0.138 Angle : 0.466 7.803 14175 Z= 0.237 Chirality : 0.037 0.121 1767 Planarity : 0.003 0.026 1677 Dihedral : 8.438 65.273 2064 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.23 % Allowed : 13.03 % Favored : 85.74 % 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: 1.88 (0.25), residues: 1272 helix: 2.13 (0.18), residues: 924 sheet: -0.69 (0.73), residues: 60 loop : -1.33 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.000 0.000 HIS B 296 PHE 0.007 0.001 PHE A 240 TYR 0.007 0.001 TYR C 257 ARG 0.001 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.162 Fit side-chains REVERT: A 165 LYS cc_start: 0.8060 (pttt) cc_final: 0.7565 (ptmm) REVERT: A 258 MET cc_start: 0.7729 (ttp) cc_final: 0.7406 (ttt) REVERT: A 449 MET cc_start: 0.7682 (ttp) cc_final: 0.7340 (ttt) REVERT: B 39 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7440 (mtp180) REVERT: B 165 LYS cc_start: 0.8115 (pttt) cc_final: 0.7547 (ptmm) REVERT: B 258 MET cc_start: 0.7750 (ttp) cc_final: 0.7463 (ttt) REVERT: C 39 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7395 (mtp180) REVERT: C 165 LYS cc_start: 0.8087 (pttt) cc_final: 0.7571 (ptmm) REVERT: C 258 MET cc_start: 0.7787 (ttp) cc_final: 0.7419 (ttt) REVERT: C 315 ARG cc_start: 0.7067 (mpt-90) cc_final: 0.6808 (tpp-160) REVERT: C 449 MET cc_start: 0.7601 (ttp) cc_final: 0.7281 (ttp) outliers start: 13 outliers final: 11 residues processed: 145 average time/residue: 0.2453 time to fit residues: 49.4059 Evaluate side-chains 144 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 0.0030 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10497 Z= 0.131 Angle : 0.466 9.323 14175 Z= 0.235 Chirality : 0.037 0.145 1767 Planarity : 0.003 0.026 1677 Dihedral : 8.263 64.440 2064 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.23 % Allowed : 13.31 % Favored : 85.46 % 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: 1.85 (0.25), residues: 1272 helix: 2.12 (0.18), residues: 939 sheet: -0.68 (0.73), residues: 60 loop : -1.57 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.000 0.000 HIS B 296 PHE 0.006 0.001 PHE C 239 TYR 0.007 0.001 TYR B 162 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.138 Fit side-chains REVERT: A 165 LYS cc_start: 0.8043 (pttt) cc_final: 0.7549 (ptmm) REVERT: A 258 MET cc_start: 0.7711 (ttp) cc_final: 0.7392 (ttt) REVERT: A 449 MET cc_start: 0.7706 (ttp) cc_final: 0.7378 (ttt) REVERT: B 39 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7451 (mtp180) REVERT: B 165 LYS cc_start: 0.8104 (pttt) cc_final: 0.7555 (ptmm) REVERT: B 255 MET cc_start: 0.8475 (mmm) cc_final: 0.8223 (mmm) REVERT: B 258 MET cc_start: 0.7729 (ttp) cc_final: 0.7430 (ttt) REVERT: C 39 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7386 (mtp180) REVERT: C 165 LYS cc_start: 0.8079 (pttt) cc_final: 0.7561 (ptmm) REVERT: C 255 MET cc_start: 0.8654 (mmm) cc_final: 0.8378 (mmm) REVERT: C 258 MET cc_start: 0.7781 (ttp) cc_final: 0.7408 (ttt) REVERT: C 315 ARG cc_start: 0.7056 (mpt-90) cc_final: 0.6802 (tpp-160) REVERT: C 449 MET cc_start: 0.7592 (ttp) cc_final: 0.7254 (ttp) outliers start: 13 outliers final: 8 residues processed: 145 average time/residue: 0.2347 time to fit residues: 47.5758 Evaluate side-chains 144 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0050 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- 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: 0.7946 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10497 Z= 0.204 Angle : 0.505 8.948 14175 Z= 0.257 Chirality : 0.039 0.183 1767 Planarity : 0.003 0.026 1677 Dihedral : 8.547 63.610 2064 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.85 % Allowed : 13.88 % Favored : 85.27 % 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: 1.77 (0.25), residues: 1272 helix: 1.88 (0.17), residues: 963 sheet: -0.67 (0.73), residues: 60 loop : -1.16 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.000 0.000 HIS A 296 PHE 0.012 0.001 PHE C 240 TYR 0.007 0.001 TYR B 162 ARG 0.002 0.000 ARG C 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.160 Fit side-chains REVERT: A 165 LYS cc_start: 0.8078 (pttt) cc_final: 0.7562 (ptmm) REVERT: A 258 MET cc_start: 0.7762 (ttp) cc_final: 0.7436 (ttt) REVERT: A 449 MET cc_start: 0.7739 (ttp) cc_final: 0.7406 (ttt) REVERT: B 39 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7457 (mtp180) REVERT: B 165 LYS cc_start: 0.8131 (pttt) cc_final: 0.7561 (ptmm) REVERT: B 258 MET cc_start: 0.7738 (ttp) cc_final: 0.7465 (ttt) REVERT: C 39 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7487 (mtp180) REVERT: C 165 LYS cc_start: 0.8103 (pttt) cc_final: 0.7567 (ptmm) REVERT: C 258 MET cc_start: 0.7689 (ttp) cc_final: 0.7334 (ttt) REVERT: C 315 ARG cc_start: 0.7064 (mpt-90) cc_final: 0.6802 (tpp-160) outliers start: 9 outliers final: 9 residues processed: 140 average time/residue: 0.2479 time to fit residues: 48.5492 Evaluate side-chains 144 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.152267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102400 restraints weight = 11025.909| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.85 r_work: 0.2781 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10497 Z= 0.152 Angle : 0.480 9.164 14175 Z= 0.243 Chirality : 0.037 0.168 1767 Planarity : 0.003 0.026 1677 Dihedral : 8.399 63.398 2064 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.85 % Allowed : 14.16 % Favored : 84.99 % 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: 1.78 (0.25), residues: 1272 helix: 2.01 (0.18), residues: 945 sheet: -0.65 (0.73), residues: 60 loop : -1.45 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.000 0.000 HIS B 296 PHE 0.008 0.001 PHE C 159 TYR 0.008 0.001 TYR B 162 ARG 0.002 0.000 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.99 seconds wall clock time: 42 minutes 51.25 seconds (2571.25 seconds total)