Starting phenix.real_space_refine on Tue Aug 6 06:54:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xnh_38504/08_2024/8xnh_38504.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xnh_38504/08_2024/8xnh_38504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xnh_38504/08_2024/8xnh_38504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xnh_38504/08_2024/8xnh_38504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xnh_38504/08_2024/8xnh_38504.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xnh_38504/08_2024/8xnh_38504.cif" } resolution = 2.3 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= 0.026 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9962 2.51 5 N 2568 2.21 5 O 3104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 103": "OD1" <-> "OD2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 452": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 859 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 6, 'TRANS': 104} Chain: "G" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1012 Classifications: {'peptide': 130} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 122} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "I" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1012 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 343 residue: pdb=" N ASP D 1 " occ=0.71 ... (6 atoms not shown) pdb=" OD2 ASP D 1 " occ=0.02 residue: pdb=" N GLN D 3 " occ=0.88 ... (7 atoms not shown) pdb=" NE2 GLN D 3 " occ=0.63 residue: pdb=" N THR D 5 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR D 5 " occ=0.82 residue: pdb=" N GLN D 6 " occ=0.44 ... (7 atoms not shown) pdb=" NE2 GLN D 6 " occ=0.21 residue: pdb=" N SER D 7 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER D 7 " occ=0.42 residue: pdb=" N PRO D 8 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO D 8 " occ=0.58 residue: pdb=" N SER D 9 " occ=0.24 ... (4 atoms not shown) pdb=" OG SER D 9 " occ=0.00 residue: pdb=" N SER D 10 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER D 10 " occ=0.32 residue: pdb=" N LEU D 11 " occ=0.24 ... (6 atoms not shown) pdb=" CD2 LEU D 11 " occ=0.54 residue: pdb=" N SER D 12 " occ=0.11 ... (4 atoms not shown) pdb=" OG SER D 12 " occ=0.28 residue: pdb=" N ALA D 13 " occ=0.26 ... (3 atoms not shown) pdb=" CB ALA D 13 " occ=0.68 residue: pdb=" N SER D 14 " occ=0.19 ... (4 atoms not shown) pdb=" OG SER D 14 " occ=0.50 ... (remaining 331 not shown) Time building chain proxies: 10.59, per 1000 atoms: 0.67 Number of scatterers: 15706 At special positions: 0 Unit cell: (107.07, 142.76, 155.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3104 8.00 N 2568 7.00 C 9962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 87 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 414 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 414 " " NAG C 601 " - " ASN C 99 " " NAG C 602 " - " ASN C 414 " Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 2.8 seconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 32 sheets defined 28.0% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.572A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.791A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.745A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.740A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 4.544A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.661A pdb=" N ILE A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.754A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.717A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 357 through 358 No H-bonds generated for 'chain 'A' and resid 357 through 358' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.500A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.820A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.735A pdb=" N THR G 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'I' and resid 65 through 69 removed outlier: 3.520A pdb=" N VAL I 69 " --> pdb=" O LYS I 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 3.561A pdb=" N ILE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.882A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.889A pdb=" N ASN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 3.648A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 4.489A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.514A pdb=" N THR B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.543A pdb=" N THR B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.809A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.903A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.511A pdb=" N SER B 440 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 441 " --> pdb=" O TYR B 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 437 through 441' Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.766A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.526A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 100 removed outlier: 3.582A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 3.816A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 145 removed outlier: 4.206A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 142 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.637A pdb=" N THR C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 187 " --> pdb=" O VAL C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'C' and resid 191 through 215 removed outlier: 4.762A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.853A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.557A pdb=" N THR C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.519A pdb=" N LYS C 362 " --> pdb=" O SER C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 452 through 471 removed outlier: 3.912A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 17.835A pdb=" N THR A 168 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N THR A 54 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N TYR A 170 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASP A 56 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N LEU A 172 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 58 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.280A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400 removed outlier: 6.796A pdb=" N ILE A 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.698A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.652A pdb=" N THR E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.530A pdb=" N TYR E 86 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 84 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR E 96 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.580A pdb=" N ILE F 75 " --> pdb=" O VAL F 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.544A pdb=" N ALA F 13 " --> pdb=" O ASP F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.921A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 96 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.561A pdb=" N LEU G 20 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL G 12 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG G 34 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL G 12 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS G 97 " --> pdb=" O TRP G 119 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP G 119 " --> pdb=" O CYS G 97 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG G 99 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.625A pdb=" N SER H 72 " --> pdb=" O SER H 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N ALA H 93 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE H 38 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG H 34 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN H 60 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N ALA H 93 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG H 99 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.589A pdb=" N GLN I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER I 72 " --> pdb=" O SER I 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.689A pdb=" N VAL I 123 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL I 125 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA I 93 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG I 34 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.689A pdb=" N VAL I 123 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL I 125 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA I 93 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG I 99 " --> pdb=" O ASP I 117 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP I 117 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 158 through 160 removed outlier: 11.950A pdb=" N TYR B 170 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASP B 56 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU B 172 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 58 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 263 through 270 removed outlier: 6.676A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 101 through 102 removed outlier: 4.583A pdb=" N CYS C 392 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AD2, first strand: chain 'B' and resid 301 through 302 removed outlier: 3.577A pdb=" N PHE B 301 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 158 through 162 removed outlier: 11.364A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.244A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE C 284 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASN C 51 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR C 286 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS C 49 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 301 through 302 642 hydrogen bonds defined for protein. 1689 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: 5.87 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5013 1.34 - 1.46: 3494 1.46 - 1.58: 7380 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 15989 Sorted by residual: bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" CB VAL G 100 " pdb=" CG1 VAL G 100 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CA THR A 88 " pdb=" C THR A 88 " ideal model delta sigma weight residual 1.520 1.537 -0.017 1.23e-02 6.61e+03 1.91e+00 bond pdb=" CA THR C 88 " pdb=" C THR C 88 " ideal model delta sigma weight residual 1.520 1.536 -0.016 1.23e-02 6.61e+03 1.63e+00 bond pdb=" CA THR F 20 " pdb=" C THR F 20 " ideal model delta sigma weight residual 1.519 1.533 -0.014 1.14e-02 7.69e+03 1.54e+00 ... (remaining 15984 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 364 106.24 - 113.17: 8891 113.17 - 120.11: 5336 120.11 - 127.05: 7030 127.05 - 133.99: 131 Bond angle restraints: 21752 Sorted by residual: angle pdb=" N GLU C 95 " pdb=" CA GLU C 95 " pdb=" CB GLU C 95 " ideal model delta sigma weight residual 110.32 118.02 -7.70 1.70e+00 3.46e-01 2.05e+01 angle pdb=" CA GLU C 95 " pdb=" CB GLU C 95 " pdb=" CG GLU C 95 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C SER D 9 " pdb=" N SER D 10 " pdb=" CA SER D 10 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" C SER A 50 " pdb=" N ASN A 51 " pdb=" CA ASN A 51 " ideal model delta sigma weight residual 121.80 128.75 -6.95 2.44e+00 1.68e-01 8.12e+00 angle pdb=" CA GLY H 50 " pdb=" C GLY H 50 " pdb=" N TYR H 51 " ideal model delta sigma weight residual 114.48 117.79 -3.31 1.19e+00 7.06e-01 7.75e+00 ... (remaining 21747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9053 17.97 - 35.94: 562 35.94 - 53.91: 104 53.91 - 71.88: 30 71.88 - 89.85: 14 Dihedral angle restraints: 9763 sinusoidal: 3856 harmonic: 5907 Sorted by residual: dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -147.73 61.73 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -146.28 60.28 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 150.10 -57.10 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 9760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1478 0.033 - 0.066: 694 0.066 - 0.099: 257 0.099 - 0.133: 154 0.133 - 0.166: 19 Chirality restraints: 2602 Sorted by residual: chirality pdb=" CA ILE G 38 " pdb=" N ILE G 38 " pdb=" C ILE G 38 " pdb=" CB ILE G 38 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA GLU C 95 " pdb=" N GLU C 95 " pdb=" C GLU C 95 " pdb=" CB GLU C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA VAL A 312 " pdb=" N VAL A 312 " pdb=" C VAL A 312 " pdb=" CB VAL A 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2599 not shown) Planarity restraints: 2746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 120 " 0.032 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO I 121 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO I 121 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 121 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 62 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO H 63 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 63 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 63 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 446 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO B 447 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " -0.024 5.00e-02 4.00e+02 ... (remaining 2743 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 330 2.71 - 3.26: 14561 3.26 - 3.81: 23360 3.81 - 4.35: 31262 4.35 - 4.90: 51667 Nonbonded interactions: 121180 Sorted by model distance: nonbonded pdb=" O GLY F 30 " pdb=" OH TYR F 71 " model vdw 2.164 3.040 nonbonded pdb=" O GLY E 30 " pdb=" OH TYR E 71 " model vdw 2.180 3.040 nonbonded pdb=" NZ LYS C 60 " pdb=" O ILE C 62 " model vdw 2.257 3.120 nonbonded pdb=" O GLY D 30 " pdb=" OH TYR D 71 " model vdw 2.315 3.040 nonbonded pdb=" OG SER I 36 " pdb=" O GLY I 50 " model vdw 2.344 3.040 ... (remaining 121175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 107) selection = (chain 'F' and resid 1 through 107) } ncs_group { reference = (chain 'G' and resid 1 through 128) selection = chain 'H' selection = (chain 'I' and resid 1 through 128) } 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=0.00 max=1.00 mean=0.87 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: 8.570 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: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.160 Process input model: 47.460 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.004 0.046 15989 Z= 0.229 Angle : 0.663 7.695 21752 Z= 0.379 Chirality : 0.048 0.166 2602 Planarity : 0.005 0.049 2740 Dihedral : 12.739 89.850 5908 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2007 helix: 0.54 (0.25), residues: 420 sheet: 0.26 (0.23), residues: 534 loop : -1.12 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 106 HIS 0.006 0.002 HIS F 34 PHE 0.011 0.002 PHE B 212 TYR 0.014 0.002 TYR H 51 ARG 0.008 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 GLN cc_start: 0.5920 (pp30) cc_final: 0.4241 (pm20) REVERT: D 107 ARG cc_start: 0.6102 (tmm-80) cc_final: 0.5443 (tpt170) REVERT: G 53 TYR cc_start: 0.8428 (m-80) cc_final: 0.8044 (m-80) REVERT: I 38 ILE cc_start: 0.8086 (mt) cc_final: 0.7543 (tt) REVERT: I 88 THR cc_start: 0.7908 (p) cc_final: 0.7666 (m) REVERT: I 124 LEU cc_start: 0.7588 (tp) cc_final: 0.7374 (tt) outliers start: 0 outliers final: 1 residues processed: 283 average time/residue: 1.4399 time to fit residues: 444.8263 Evaluate side-chains 177 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN G 79 GLN H 79 GLN I 78 ASN B 393 GLN B 395 GLN C 290 GLN C 303 ASN C 393 GLN C 395 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 15989 Z= 0.457 Angle : 0.708 8.279 21752 Z= 0.384 Chirality : 0.052 0.172 2602 Planarity : 0.006 0.052 2740 Dihedral : 5.289 34.549 2294 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.84 % Allowed : 8.59 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: -0.36 (0.18), residues: 2007 helix: 1.23 (0.26), residues: 405 sheet: 0.25 (0.21), residues: 568 loop : -1.13 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 106 HIS 0.005 0.002 HIS A 29 PHE 0.017 0.002 PHE C 212 TYR 0.020 0.002 TYR H 33 ARG 0.006 0.001 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.5703 (mpt) REVERT: D 36 TYR cc_start: 0.7531 (m-80) cc_final: 0.7071 (m-80) REVERT: D 107 ARG cc_start: 0.5905 (tmm-80) cc_final: 0.5310 (tpm170) REVERT: E 82 ASP cc_start: 0.7311 (p0) cc_final: 0.7044 (p0) REVERT: G 34 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7174 (ptt-90) REVERT: H 74 ASP cc_start: 0.8339 (t0) cc_final: 0.8048 (t0) REVERT: I 38 ILE cc_start: 0.8033 (mt) cc_final: 0.7485 (tt) REVERT: I 39 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7361 (ppt-90) REVERT: I 77 LYS cc_start: 0.7380 (tmtm) cc_final: 0.7169 (ptmm) REVERT: I 88 THR cc_start: 0.7993 (p) cc_final: 0.7633 (m) REVERT: B 290 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: C 61 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.5878 (mpt) outliers start: 51 outliers final: 17 residues processed: 215 average time/residue: 1.3548 time to fit residues: 320.5906 Evaluate side-chains 188 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN H 60 ASN I 40 GLN B 102 HIS B 182 ASN B 393 GLN B 395 GLN C 395 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15989 Z= 0.201 Angle : 0.560 9.588 21752 Z= 0.298 Chirality : 0.046 0.148 2602 Planarity : 0.005 0.045 2740 Dihedral : 4.620 20.500 2292 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.29 % Allowed : 11.04 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2007 helix: 1.65 (0.26), residues: 408 sheet: 0.41 (0.22), residues: 572 loop : -1.03 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 106 HIS 0.003 0.001 HIS F 34 PHE 0.011 0.001 PHE B 301 TYR 0.018 0.001 TYR H 33 ARG 0.005 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.5517 (mpt) REVERT: D 79 GLN cc_start: 0.8072 (mm110) cc_final: 0.7849 (mm-40) REVERT: D 88 GLN cc_start: 0.8204 (tt0) cc_final: 0.8000 (tt0) REVERT: D 107 ARG cc_start: 0.5938 (tmm-80) cc_final: 0.5441 (tpm170) REVERT: E 37 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: E 82 ASP cc_start: 0.7137 (p0) cc_final: 0.6806 (p0) REVERT: E 105 ILE cc_start: 0.2770 (mp) cc_final: 0.2400 (tp) REVERT: F 17 ASP cc_start: 0.8056 (m-30) cc_final: 0.7792 (m-30) REVERT: H 74 ASP cc_start: 0.8360 (t0) cc_final: 0.8117 (t0) REVERT: I 38 ILE cc_start: 0.7938 (mt) cc_final: 0.7365 (tt) REVERT: I 88 THR cc_start: 0.7914 (p) cc_final: 0.7628 (m) REVERT: B 290 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6396 (mp10) outliers start: 41 outliers final: 12 residues processed: 216 average time/residue: 1.3291 time to fit residues: 316.2661 Evaluate side-chains 194 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN H 79 GLN C 395 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15989 Z= 0.321 Angle : 0.616 10.277 21752 Z= 0.328 Chirality : 0.048 0.151 2602 Planarity : 0.005 0.045 2740 Dihedral : 4.733 21.020 2292 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.29 % Allowed : 12.66 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: -0.08 (0.18), residues: 2007 helix: 1.63 (0.26), residues: 408 sheet: 0.55 (0.22), residues: 548 loop : -1.10 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 106 HIS 0.005 0.002 HIS A 102 PHE 0.012 0.002 PHE B 301 TYR 0.057 0.002 TYR I 51 ARG 0.005 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.5557 (mpt) REVERT: D 79 GLN cc_start: 0.8116 (mm110) cc_final: 0.7907 (mm110) REVERT: D 107 ARG cc_start: 0.5929 (tmm-80) cc_final: 0.5312 (tpm170) REVERT: E 37 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: E 82 ASP cc_start: 0.7136 (p0) cc_final: 0.6805 (p0) REVERT: F 17 ASP cc_start: 0.8109 (m-30) cc_final: 0.7891 (m-30) REVERT: G 68 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7173 (mtp180) REVERT: I 38 ILE cc_start: 0.7923 (mt) cc_final: 0.7332 (tt) REVERT: I 88 THR cc_start: 0.7915 (p) cc_final: 0.7642 (m) REVERT: I 117 ASP cc_start: 0.7599 (p0) cc_final: 0.7322 (p0) REVERT: B 290 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6458 (mp10) outliers start: 41 outliers final: 17 residues processed: 210 average time/residue: 1.3126 time to fit residues: 304.0310 Evaluate side-chains 190 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 78 optimal weight: 0.0170 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 37 GLN E 88 GLN H 78 ASN I 60 ASN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15989 Z= 0.270 Angle : 0.593 10.278 21752 Z= 0.313 Chirality : 0.047 0.149 2602 Planarity : 0.005 0.044 2740 Dihedral : 4.642 21.020 2292 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 12.77 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: -0.11 (0.18), residues: 2007 helix: 1.66 (0.26), residues: 408 sheet: 0.43 (0.22), residues: 558 loop : -1.09 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 106 HIS 0.005 0.001 HIS F 34 PHE 0.012 0.001 PHE B 301 TYR 0.019 0.002 TYR H 51 ARG 0.006 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.5623 (mpt) REVERT: D 79 GLN cc_start: 0.8130 (mm110) cc_final: 0.7916 (mm110) REVERT: D 107 ARG cc_start: 0.5892 (tmm-80) cc_final: 0.5299 (tpm170) REVERT: E 37 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6318 (tt0) REVERT: E 82 ASP cc_start: 0.7012 (p0) cc_final: 0.6758 (p0) REVERT: H 74 ASP cc_start: 0.8373 (t0) cc_final: 0.8078 (t0) REVERT: I 38 ILE cc_start: 0.7895 (mt) cc_final: 0.7309 (tt) REVERT: I 88 THR cc_start: 0.7877 (p) cc_final: 0.7646 (m) REVERT: I 117 ASP cc_start: 0.7622 (p0) cc_final: 0.7373 (p0) REVERT: B 290 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.6436 (mp10) outliers start: 49 outliers final: 24 residues processed: 203 average time/residue: 1.3208 time to fit residues: 296.7332 Evaluate side-chains 191 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 37 GLN H 78 ASN C 395 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15989 Z= 0.317 Angle : 0.618 10.116 21752 Z= 0.326 Chirality : 0.048 0.150 2602 Planarity : 0.005 0.046 2740 Dihedral : 4.696 21.473 2292 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.18 % Allowed : 12.83 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: -0.17 (0.18), residues: 2007 helix: 1.62 (0.26), residues: 408 sheet: 0.40 (0.22), residues: 558 loop : -1.14 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 106 HIS 0.004 0.001 HIS F 34 PHE 0.013 0.002 PHE B 301 TYR 0.020 0.002 TYR D 49 ARG 0.007 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 169 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.5603 (mpt) REVERT: D 86 TYR cc_start: 0.6636 (m-80) cc_final: 0.6368 (m-80) REVERT: D 107 ARG cc_start: 0.5826 (tmm-80) cc_final: 0.5257 (tpm170) REVERT: E 37 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.6028 (tt0) REVERT: E 82 ASP cc_start: 0.7012 (p0) cc_final: 0.6681 (p0) REVERT: F 106 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8191 (ttmm) REVERT: G 68 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7233 (mtp180) REVERT: I 21 THR cc_start: 0.8567 (p) cc_final: 0.8366 (t) REVERT: I 38 ILE cc_start: 0.7928 (mt) cc_final: 0.7335 (tt) REVERT: I 39 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7359 (ppt-90) REVERT: I 88 THR cc_start: 0.7898 (p) cc_final: 0.7658 (m) REVERT: I 117 ASP cc_start: 0.7757 (p0) cc_final: 0.7521 (p0) REVERT: B 290 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6505 (mp10) outliers start: 57 outliers final: 30 residues processed: 205 average time/residue: 1.2927 time to fit residues: 292.8946 Evaluate side-chains 199 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 37 GLN H 78 ASN C 395 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15989 Z= 0.328 Angle : 0.626 9.112 21752 Z= 0.332 Chirality : 0.048 0.156 2602 Planarity : 0.005 0.046 2740 Dihedral : 4.738 21.808 2292 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.35 % Allowed : 12.88 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: -0.17 (0.18), residues: 2007 helix: 1.63 (0.26), residues: 408 sheet: 0.46 (0.22), residues: 550 loop : -1.17 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 106 HIS 0.004 0.001 HIS F 34 PHE 0.013 0.002 PHE B 301 TYR 0.021 0.002 TYR D 49 ARG 0.007 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 167 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.5630 (mpt) REVERT: D 107 ARG cc_start: 0.5859 (tmm-80) cc_final: 0.5183 (tpm170) REVERT: F 17 ASP cc_start: 0.8014 (m-30) cc_final: 0.7534 (m-30) REVERT: F 106 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8179 (ttmm) REVERT: G 68 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7193 (mtp180) REVERT: I 21 THR cc_start: 0.8583 (p) cc_final: 0.8370 (t) REVERT: I 38 ILE cc_start: 0.7918 (mt) cc_final: 0.7335 (tt) REVERT: I 39 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7356 (ppt-90) REVERT: I 88 THR cc_start: 0.7916 (p) cc_final: 0.7658 (m) REVERT: I 117 ASP cc_start: 0.7780 (p0) cc_final: 0.7570 (p0) REVERT: B 290 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6501 (mp10) outliers start: 60 outliers final: 37 residues processed: 202 average time/residue: 1.3080 time to fit residues: 291.3416 Evaluate side-chains 201 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 37 GLN H 78 ASN C 395 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15989 Z= 0.273 Angle : 0.607 9.002 21752 Z= 0.322 Chirality : 0.047 0.149 2602 Planarity : 0.005 0.045 2740 Dihedral : 4.664 21.493 2292 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.96 % Allowed : 14.11 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: -0.13 (0.18), residues: 2007 helix: 1.70 (0.26), residues: 408 sheet: 0.48 (0.22), residues: 546 loop : -1.15 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 106 HIS 0.004 0.001 HIS F 34 PHE 0.012 0.001 PHE B 301 TYR 0.021 0.002 TYR D 49 ARG 0.007 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 164 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.5605 (mpt) REVERT: D 107 ARG cc_start: 0.5704 (tmm-80) cc_final: 0.5060 (tpm170) REVERT: F 1 ASP cc_start: 0.7059 (m-30) cc_final: 0.6737 (m-30) REVERT: F 17 ASP cc_start: 0.7988 (m-30) cc_final: 0.7511 (m-30) REVERT: F 106 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8168 (ttmm) REVERT: G 68 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: I 21 THR cc_start: 0.8592 (p) cc_final: 0.8374 (t) REVERT: I 38 ILE cc_start: 0.7919 (mt) cc_final: 0.7333 (tt) REVERT: I 39 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7360 (ppt-90) REVERT: I 88 THR cc_start: 0.7889 (p) cc_final: 0.7656 (m) REVERT: I 117 ASP cc_start: 0.7694 (p0) cc_final: 0.7466 (p0) REVERT: B 290 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.6445 (mp10) outliers start: 53 outliers final: 37 residues processed: 198 average time/residue: 1.3651 time to fit residues: 299.5150 Evaluate side-chains 202 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.0670 chunk 166 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 54 optimal weight: 0.0670 chunk 160 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN C 395 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15989 Z= 0.178 Angle : 0.569 9.334 21752 Z= 0.298 Chirality : 0.045 0.152 2602 Planarity : 0.004 0.042 2740 Dihedral : 4.375 20.012 2292 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.18 % Allowed : 15.06 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2007 helix: 1.96 (0.26), residues: 408 sheet: 0.53 (0.22), residues: 552 loop : -1.07 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 106 HIS 0.003 0.001 HIS E 34 PHE 0.011 0.001 PHE B 301 TYR 0.022 0.001 TYR D 49 ARG 0.007 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 172 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.5531 (mpt) REVERT: D 107 ARG cc_start: 0.5621 (tmm-80) cc_final: 0.5093 (tpm170) REVERT: F 17 ASP cc_start: 0.7958 (m-30) cc_final: 0.7458 (m-30) REVERT: I 21 THR cc_start: 0.8567 (p) cc_final: 0.8355 (t) REVERT: I 38 ILE cc_start: 0.7878 (mt) cc_final: 0.7303 (tt) REVERT: I 39 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7355 (ppt-90) REVERT: I 77 LYS cc_start: 0.7066 (ptmm) cc_final: 0.6819 (ptmm) REVERT: I 117 ASP cc_start: 0.7660 (p0) cc_final: 0.7440 (p0) outliers start: 39 outliers final: 22 residues processed: 194 average time/residue: 1.3803 time to fit residues: 294.2767 Evaluate side-chains 186 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN H 78 ASN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15989 Z= 0.206 Angle : 0.581 10.212 21752 Z= 0.304 Chirality : 0.046 0.151 2602 Planarity : 0.004 0.041 2740 Dihedral : 4.350 20.131 2292 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.90 % Allowed : 15.11 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % 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: 0.10 (0.19), residues: 2007 helix: 2.03 (0.26), residues: 408 sheet: 0.54 (0.22), residues: 554 loop : -1.04 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 106 HIS 0.004 0.001 HIS F 34 PHE 0.011 0.001 PHE H 80 TYR 0.023 0.001 TYR D 49 ARG 0.007 0.001 ARG C 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.5533 (mpt) REVERT: D 107 ARG cc_start: 0.5542 (tmm-80) cc_final: 0.5025 (tpm170) REVERT: F 17 ASP cc_start: 0.7944 (m-30) cc_final: 0.7450 (m-30) REVERT: I 21 THR cc_start: 0.8616 (p) cc_final: 0.8398 (t) REVERT: I 38 ILE cc_start: 0.7879 (mt) cc_final: 0.7286 (tt) REVERT: I 39 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7354 (ppt-90) REVERT: I 77 LYS cc_start: 0.7001 (ptmm) cc_final: 0.6771 (ptmm) REVERT: I 117 ASP cc_start: 0.7664 (p0) cc_final: 0.7433 (p0) outliers start: 34 outliers final: 23 residues processed: 183 average time/residue: 1.3869 time to fit residues: 279.0083 Evaluate side-chains 184 residues out of total 1793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 48 optimal weight: 0.0030 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN H 78 ASN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083924 restraints weight = 34189.024| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.54 r_work: 0.3103 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 339 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 285 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15989 Z= 0.170 Angle : 0.566 13.131 21752 Z= 0.294 Chirality : 0.045 0.191 2602 Planarity : 0.004 0.040 2740 Dihedral : 4.206 19.672 2292 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.73 % Allowed : 15.50 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 2007 helix: 2.12 (0.26), residues: 408 sheet: 0.55 (0.22), residues: 565 loop : -0.97 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 106 HIS 0.003 0.001 HIS E 34 PHE 0.010 0.001 PHE B 301 TYR 0.022 0.001 TYR D 49 ARG 0.007 0.001 ARG C 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6387.58 seconds wall clock time: 112 minutes 16.22 seconds (6736.22 seconds total)