Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 17:56:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/04_2023/7nsg_12566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/04_2023/7nsg_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_12566/04_2023/7nsg_12566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/04_2023/7nsg_12566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/04_2023/7nsg_12566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsg_12566/04_2023/7nsg_12566.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 104 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: 104 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: 104 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: 104 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: 104 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: 104 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: 6.25, per 1000 atoms: 0.60 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 1.6 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: 0.49 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: 2.93 Time building geometry restraints manager: 4.58 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: 5688 17.90 - 35.79: 483 35.79 - 53.69: 75 53.69 - 71.58: 18 71.58 - 89.48: 3 Dihedral angle restraints: 6267 sinusoidal: 2562 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 6264 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: 0.670 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: 2.770 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.760 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- 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 : 13.503 89.476 3873 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 % 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 *********************** 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 : 1.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2862 time to fit residues: 61.8499 Evaluate side-chains 128 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7406 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 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: 0.8786 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10497 Z= 0.161 Angle : 0.527 10.763 14175 Z= 0.273 Chirality : 0.037 0.134 1767 Planarity : 0.004 0.036 1677 Dihedral : 8.372 57.570 1677 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 1.04 % 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: -0.83 (0.23), residues: 1272 helix: 0.07 (0.17), residues: 966 sheet: -0.95 (0.76), residues: 60 loop : -2.58 (0.32), residues: 246 *********************** 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 157 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.262 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 0.2349 time to fit residues: 49.7003 Evaluate side-chains 139 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0944 time to fit residues: 2.6446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 0.0770 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.1680 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= 0.162 Angle : 0.497 8.854 14175 Z= 0.253 Chirality : 0.037 0.126 1767 Planarity : 0.003 0.031 1677 Dihedral : 7.837 58.430 1677 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.23 % 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: 0.24 (0.24), residues: 1272 helix: 0.96 (0.18), residues: 954 sheet: -0.79 (0.74), residues: 60 loop : -2.55 (0.32), residues: 258 *********************** 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 155 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.228 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 149 average time/residue: 0.2489 time to fit residues: 51.6652 Evaluate side-chains 143 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0971 time to fit residues: 2.8100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.0020 chunk 124 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 161 GLN C 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.002 0.021 10497 Z= 0.117 Angle : 0.460 7.976 14175 Z= 0.233 Chirality : 0.036 0.124 1767 Planarity : 0.003 0.028 1677 Dihedral : 7.465 59.642 1677 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 1.13 % 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: 1.03 (0.25), residues: 1272 helix: 1.57 (0.18), residues: 936 sheet: -0.72 (0.73), residues: 60 loop : -2.08 (0.34), residues: 276 *********************** 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 164 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 1.153 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 162 average time/residue: 0.2527 time to fit residues: 56.1876 Evaluate side-chains 141 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0912 time to fit residues: 1.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7921 moved from start: 0.2070 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= 0.148 Angle : 0.479 9.182 14175 Z= 0.240 Chirality : 0.037 0.124 1767 Planarity : 0.003 0.028 1677 Dihedral : 7.465 59.617 1677 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 1.13 % 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: 1.21 (0.25), residues: 1272 helix: 1.57 (0.18), residues: 975 sheet: -0.78 (0.73), residues: 60 loop : -1.97 (0.37), residues: 237 *********************** 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 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.252 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 149 average time/residue: 0.2464 time to fit residues: 51.7322 Evaluate side-chains 146 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1598 time to fit residues: 3.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 10497 Z= 0.132 Angle : 0.467 8.597 14175 Z= 0.236 Chirality : 0.037 0.124 1767 Planarity : 0.003 0.028 1677 Dihedral : 7.397 59.801 1677 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.38 % 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: 1.66 (0.25), residues: 1272 helix: 1.90 (0.18), residues: 960 sheet: -0.77 (0.73), residues: 60 loop : -1.56 (0.37), residues: 252 *********************** 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 143 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.140 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.2388 time to fit residues: 47.7450 Evaluate side-chains 138 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0953 time to fit residues: 1.8262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.2244 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= 0.145 Angle : 0.474 8.380 14175 Z= 0.240 Chirality : 0.037 0.125 1767 Planarity : 0.003 0.029 1677 Dihedral : 7.409 59.721 1677 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.76 % 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: 1.59 (0.25), residues: 1272 helix: 1.92 (0.18), residues: 963 sheet: -0.83 (0.72), residues: 60 loop : -1.98 (0.37), residues: 249 *********************** 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 143 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.085 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 142 average time/residue: 0.2312 time to fit residues: 46.1055 Evaluate side-chains 136 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0965 time to fit residues: 1.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 0.0070 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 10497 Z= 0.137 Angle : 0.467 8.237 14175 Z= 0.237 Chirality : 0.037 0.125 1767 Planarity : 0.003 0.029 1677 Dihedral : 7.343 59.672 1677 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.38 % 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: 1.70 (0.25), residues: 1272 helix: 2.00 (0.18), residues: 963 sheet: -0.81 (0.73), residues: 60 loop : -1.94 (0.37), residues: 249 *********************** 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 140 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.074 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 139 average time/residue: 0.2282 time to fit residues: 45.6025 Evaluate side-chains 133 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0920 time to fit residues: 2.1276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 10497 Z= 0.155 Angle : 0.476 8.038 14175 Z= 0.242 Chirality : 0.037 0.125 1767 Planarity : 0.003 0.029 1677 Dihedral : 7.391 59.296 1677 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.38 % 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: 1.83 (0.25), residues: 1272 helix: 1.92 (0.17), residues: 987 sheet: -0.81 (0.73), residues: 60 loop : -1.43 (0.39), residues: 225 *********************** 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 136 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.172 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 134 average time/residue: 0.2317 time to fit residues: 44.6426 Evaluate side-chains 131 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0958 time to fit residues: 2.0382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0010 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.0770 chunk 128 optimal weight: 0.0470 chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.2565 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= 0.120 Angle : 0.458 8.306 14175 Z= 0.232 Chirality : 0.037 0.129 1767 Planarity : 0.003 0.029 1677 Dihedral : 7.059 58.131 1677 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.00 % 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: 2.14 (0.25), residues: 1272 helix: 2.28 (0.18), residues: 942 sheet: -0.78 (0.73), residues: 60 loop : -1.24 (0.36), residues: 270 ********************** 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 134 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1896 time to fit residues: 39.4174 Evaluate side-chains 123 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.151160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101768 restraints weight = 11737.696| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.85 r_work: 0.2773 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 10497 Z= 0.191 Angle : 0.502 9.471 14175 Z= 0.253 Chirality : 0.038 0.171 1767 Planarity : 0.003 0.028 1677 Dihedral : 7.368 58.482 1677 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.00 % 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: 1.87 (0.25), residues: 1272 helix: 1.95 (0.17), residues: 987 sheet: -0.81 (0.73), residues: 60 loop : -1.39 (0.39), residues: 225 =============================================================================== Job complete usr+sys time: 2066.33 seconds wall clock time: 38 minutes 21.30 seconds (2301.30 seconds total)