Starting phenix.real_space_refine on Sun Jun 15 06:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn6_14068/06_2025/7qn6_14068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn6_14068/06_2025/7qn6_14068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qn6_14068/06_2025/7qn6_14068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn6_14068/06_2025/7qn6_14068.map" model { file = "/net/cci-nas-00/data/ceres_data/7qn6_14068/06_2025/7qn6_14068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn6_14068/06_2025/7qn6_14068.cif" } resolution = 2.9 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= 0.003 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 92 5.16 5 C 10941 2.51 5 N 2701 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16821 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2683 Chain: "B" Number of atoms: 2764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2664 Chain: "C" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2663 Chain: "D" Number of atoms: 2716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2721 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2592 Classifications: {'peptide': 324} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ASER B 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 209 " occ=0.50 residue: pdb=" N ALEU B 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 214 " occ=0.50 residue: pdb=" N ASER B 229 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 229 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ASER D 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 209 " occ=0.50 Time building chain proxies: 14.83, per 1000 atoms: 0.88 Number of scatterers: 16821 At special positions: 0 Unit cell: (118.272, 135.296, 124.544, 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 92 16.00 O 3087 8.00 N 2701 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG E 501 " - " ASN E 103 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN C 149 " " NAG I 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 80 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 5.15 Conformation dependent library (CDL) restraints added in 3.6 seconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 24 sheets defined 35.2% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.501A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.571A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.679A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 271 removed outlier: 3.733A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 Processing helix chain 'A' and resid 423 through 446 removed outlier: 3.525A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.500A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.572A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.678A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.732A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 307 Processing helix chain 'B' and resid 423 through 446 removed outlier: 3.525A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.501A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.572A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.678A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 removed outlier: 3.733A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.524A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.500A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.570A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.678A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 271 removed outlier: 3.732A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 423 through 446 removed outlier: 3.524A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 119 removed outlier: 4.105A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 248 through 271 removed outlier: 3.734A pdb=" N SER E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 4.041A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 271 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 300 Processing helix chain 'E' and resid 308 through 336 Processing helix chain 'E' and resid 425 through 451 Proline residue: E 436 - end of helix Processing helix chain 'K' and resid 495 through 497 No H-bonds generated for 'chain 'K' and resid 495 through 497' Processing helix chain 'L' and resid 495 through 497 No H-bonds generated for 'chain 'L' and resid 495 through 497' Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.476A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.681A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.476A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.682A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.477A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.681A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.476A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.682A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 111 removed outlier: 3.737A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA E 129 " --> pdb=" O ALA E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 109 through 111 removed outlier: 3.737A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU E 84 " --> pdb=" O HIS E 77 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS E 77 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.978A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY K 10 " --> pdb=" O THR K 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY K 10 " --> pdb=" O THR K 509 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY L 10 " --> pdb=" O THR L 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET L 421 " --> pdb=" O ALA L 437 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA L 437 " --> pdb=" O MET L 421 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP L 423 " --> pdb=" O VAL L 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY L 10 " --> pdb=" O THR L 509 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.202A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET M 421 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA M 437 " --> pdb=" O MET M 421 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP M 423 " --> pdb=" O VAL M 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.202A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2660 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: 5.84 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5100 1.34 - 1.46: 4382 1.46 - 1.58: 7662 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 17300 Sorted by residual: bond pdb=" C10 EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.804 1.766 0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C10 EPE D 501 " pdb=" S EPE D 501 " ideal model delta sigma weight residual 1.804 1.767 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" O3S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.441 0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C10 EPE B 501 " pdb=" S EPE B 501 " ideal model delta sigma weight residual 1.804 1.768 0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" O2S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.442 0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 17295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 22935 1.12 - 2.24: 445 2.24 - 3.35: 170 3.35 - 4.47: 30 4.47 - 5.59: 15 Bond angle restraints: 23595 Sorted by residual: angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.42 5.40 3.00e+00 1.11e-01 3.25e+00 angle pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 118.82 113.57 5.25 3.00e+00 1.11e-01 3.06e+00 angle pdb=" C1 BMA H 3 " pdb=" O5 BMA H 3 " pdb=" C5 BMA H 3 " ideal model delta sigma weight residual 118.82 113.58 5.24 3.00e+00 1.11e-01 3.05e+00 angle pdb=" C1 BMA I 3 " pdb=" O5 BMA I 3 " pdb=" C5 BMA I 3 " ideal model delta sigma weight residual 118.82 113.70 5.12 3.00e+00 1.11e-01 2.92e+00 angle pdb=" CA TYR D 66 " pdb=" CB TYR D 66 " pdb=" CG TYR D 66 " ideal model delta sigma weight residual 113.90 116.88 -2.98 1.80e+00 3.09e-01 2.74e+00 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10320 23.65 - 47.30: 110 47.30 - 70.94: 8 70.94 - 94.59: 29 94.59 - 118.24: 34 Dihedral angle restraints: 10501 sinusoidal: 4495 harmonic: 6006 Sorted by residual: dihedral pdb=" N1 EPE D 501 " pdb=" C5 EPE D 501 " pdb=" C6 EPE D 501 " pdb=" N4 EPE D 501 " ideal model delta sinusoidal sigma weight residual -58.50 59.74 -118.24 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C2 EPE C 501 " pdb=" C6 EPE C 501 " pdb=" N1 EPE C 501 " pdb=" C5 EPE C 501 " ideal model delta sinusoidal sigma weight residual 58.85 -59.32 118.17 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" N1 EPE B 501 " pdb=" C5 EPE B 501 " pdb=" C6 EPE B 501 " pdb=" N4 EPE B 501 " ideal model delta sinusoidal sigma weight residual -58.50 59.53 -118.03 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 10498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2281 0.053 - 0.106: 344 0.106 - 0.158: 58 0.158 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 2.23e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.01e+01 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.75e+01 ... (remaining 2692 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.028 2.00e-02 2.50e+03 2.33e-02 6.77e+00 pdb=" C7 NAG E 501 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.038 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 256 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO E 257 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 257 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 257 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 435 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO E 436 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " 0.019 5.00e-02 4.00e+02 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1266 2.74 - 3.28: 16355 3.28 - 3.82: 28937 3.82 - 4.36: 36209 4.36 - 4.90: 61152 Nonbonded interactions: 143919 Sorted by model distance: nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP A 146 " pdb=" NE2 GLN A 148 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP B 146 " pdb=" NE2 GLN B 148 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP D 146 " pdb=" NE2 GLN D 148 " model vdw 2.325 3.120 ... (remaining 143914 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' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'B' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 48.150 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.038 17337 Z= 0.128 Angle : 0.470 9.122 23698 Z= 0.214 Chirality : 0.042 0.264 2695 Planarity : 0.003 0.059 2896 Dihedral : 12.100 118.241 6661 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.39 % Allowed : 2.47 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.20), residues: 2027 helix: 2.53 (0.21), residues: 583 sheet: 1.62 (0.22), residues: 644 loop : 1.17 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 426 HIS 0.001 0.000 HIS C 191 PHE 0.006 0.001 PHE E 115 TYR 0.015 0.001 TYR D 66 ARG 0.002 0.000 ARG A 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 9) link_NAG-ASN : angle 2.64901 ( 27) link_ALPHA1-6 : bond 0.00067 ( 4) link_ALPHA1-6 : angle 1.15856 ( 12) link_BETA1-4 : bond 0.00128 ( 12) link_BETA1-4 : angle 1.13529 ( 36) link_ALPHA1-3 : bond 0.00166 ( 4) link_ALPHA1-3 : angle 1.03980 ( 12) hydrogen bonds : bond 0.21331 ( 838) hydrogen bonds : angle 7.12400 ( 2660) SS BOND : bond 0.00051 ( 8) SS BOND : angle 0.41957 ( 16) covalent geometry : bond 0.00259 (17300) covalent geometry : angle 0.45872 (23595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 543 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.7908 (p90) cc_final: 0.7419 (p90) REVERT: A 277 TYR cc_start: 0.8246 (p90) cc_final: 0.8009 (p90) REVERT: A 306 PHE cc_start: 0.7443 (t80) cc_final: 0.6816 (t80) REVERT: A 433 PHE cc_start: 0.7807 (t80) cc_final: 0.7474 (t80) REVERT: B 304 TYR cc_start: 0.8608 (t80) cc_final: 0.8388 (t80) REVERT: C 141 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7651 (mtt-85) REVERT: C 274 LYS cc_start: 0.8012 (mttt) cc_final: 0.7778 (mptt) REVERT: C 434 THR cc_start: 0.9243 (m) cc_final: 0.8932 (p) REVERT: D 227 MET cc_start: 0.7140 (mmt) cc_final: 0.6633 (mmm) REVERT: D 243 ASN cc_start: 0.8072 (t0) cc_final: 0.7854 (t0) REVERT: D 271 THR cc_start: 0.8687 (p) cc_final: 0.8476 (p) REVERT: E 244 ARG cc_start: 0.7753 (ttt-90) cc_final: 0.7531 (ttt-90) REVERT: E 310 LEU cc_start: 0.8476 (tp) cc_final: 0.8247 (tp) REVERT: E 330 PHE cc_start: 0.7626 (t80) cc_final: 0.7324 (t80) REVERT: K 468 LEU cc_start: 0.7718 (tp) cc_final: 0.7017 (tp) REVERT: K 495 TYR cc_start: 0.8360 (m-80) cc_final: 0.8007 (m-80) REVERT: L 407 LEU cc_start: 0.8228 (mt) cc_final: 0.7938 (mm) REVERT: L 472 ASN cc_start: 0.8035 (t0) cc_final: 0.7714 (t0) outliers start: 6 outliers final: 1 residues processed: 548 average time/residue: 1.2353 time to fit residues: 754.2760 Evaluate side-chains 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 0.0060 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN D 439 ASN E 147 GLN E 200 GLN E 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081203 restraints weight = 166136.612| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 5.60 r_work: 0.2805 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17337 Z= 0.150 Angle : 0.622 7.983 23698 Z= 0.318 Chirality : 0.045 0.244 2695 Planarity : 0.004 0.072 2896 Dihedral : 12.404 112.055 2931 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.82 % Allowed : 15.82 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.19), residues: 2027 helix: 2.44 (0.21), residues: 595 sheet: 1.53 (0.21), residues: 631 loop : 1.22 (0.24), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 237 HIS 0.004 0.001 HIS E 240 PHE 0.024 0.002 PHE D 301 TYR 0.022 0.002 TYR B 244 ARG 0.011 0.001 ARG A 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 9) link_NAG-ASN : angle 2.54428 ( 27) link_ALPHA1-6 : bond 0.00749 ( 4) link_ALPHA1-6 : angle 1.75607 ( 12) link_BETA1-4 : bond 0.00253 ( 12) link_BETA1-4 : angle 1.66153 ( 36) link_ALPHA1-3 : bond 0.00829 ( 4) link_ALPHA1-3 : angle 2.08725 ( 12) hydrogen bonds : bond 0.05102 ( 838) hydrogen bonds : angle 4.95050 ( 2660) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.48990 ( 16) covalent geometry : bond 0.00327 (17300) covalent geometry : angle 0.61078 (23595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 386 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.7315 (pmm) cc_final: 0.6951 (mtm) REVERT: A 90 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: A 244 TYR cc_start: 0.8094 (p90) cc_final: 0.7527 (p90) REVERT: A 277 TYR cc_start: 0.8228 (p90) cc_final: 0.7943 (p90) REVERT: A 306 PHE cc_start: 0.8109 (t80) cc_final: 0.7457 (t80) REVERT: B 265 ASN cc_start: 0.8330 (t0) cc_final: 0.8066 (t0) REVERT: B 268 LEU cc_start: 0.8817 (mm) cc_final: 0.8593 (tm) REVERT: B 304 TYR cc_start: 0.8678 (t80) cc_final: 0.8459 (t80) REVERT: C 14 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8552 (mm-30) REVERT: C 21 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8097 (mptt) REVERT: C 141 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8237 (mtm180) REVERT: C 235 LEU cc_start: 0.8689 (tp) cc_final: 0.8424 (tt) REVERT: C 244 TYR cc_start: 0.7789 (p90) cc_final: 0.7500 (p90) REVERT: C 274 LYS cc_start: 0.8090 (mttt) cc_final: 0.7645 (mptt) REVERT: C 302 VAL cc_start: 0.8486 (p) cc_final: 0.8262 (m) REVERT: C 434 THR cc_start: 0.9167 (m) cc_final: 0.8929 (p) REVERT: D 9 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7026 (ptt) REVERT: D 182 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7430 (mp0) REVERT: D 227 MET cc_start: 0.7328 (mmt) cc_final: 0.7123 (mmm) REVERT: D 243 ASN cc_start: 0.8396 (t0) cc_final: 0.7981 (t0) REVERT: D 294 LEU cc_start: 0.8787 (mt) cc_final: 0.8371 (mp) REVERT: E 83 MET cc_start: 0.9224 (mmt) cc_final: 0.8984 (mmt) REVERT: E 260 LEU cc_start: 0.8622 (pp) cc_final: 0.8344 (mm) REVERT: E 330 PHE cc_start: 0.7644 (t80) cc_final: 0.7314 (t80) REVERT: K 495 TYR cc_start: 0.8703 (m-80) cc_final: 0.8376 (m-80) REVERT: L 3 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8495 (mp10) REVERT: L 460 ASP cc_start: 0.5823 (OUTLIER) cc_final: 0.5594 (p0) REVERT: L 469 GLU cc_start: 0.7775 (mp0) cc_final: 0.7469 (mp0) REVERT: L 472 ASN cc_start: 0.8161 (t0) cc_final: 0.7907 (t0) REVERT: M 412 SER cc_start: 0.8332 (p) cc_final: 0.7994 (p) outliers start: 66 outliers final: 27 residues processed: 411 average time/residue: 1.3331 time to fit residues: 615.0834 Evaluate side-chains 363 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 333 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN C 185 GLN E 147 GLN M 464 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.076002 restraints weight = 146882.264| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.99 r_work: 0.2717 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17337 Z= 0.187 Angle : 0.652 10.742 23698 Z= 0.326 Chirality : 0.047 0.266 2695 Planarity : 0.004 0.070 2896 Dihedral : 11.935 114.974 2929 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.04 % Allowed : 16.44 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2027 helix: 1.99 (0.20), residues: 595 sheet: 1.50 (0.22), residues: 584 loop : 0.87 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 237 HIS 0.004 0.001 HIS B 107 PHE 0.025 0.002 PHE A 433 TYR 0.027 0.002 TYR D 299 ARG 0.007 0.001 ARG D 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00797 ( 9) link_NAG-ASN : angle 2.80060 ( 27) link_ALPHA1-6 : bond 0.00859 ( 4) link_ALPHA1-6 : angle 1.76907 ( 12) link_BETA1-4 : bond 0.00279 ( 12) link_BETA1-4 : angle 1.80657 ( 36) link_ALPHA1-3 : bond 0.00984 ( 4) link_ALPHA1-3 : angle 1.83925 ( 12) hydrogen bonds : bond 0.04415 ( 838) hydrogen bonds : angle 4.72608 ( 2660) SS BOND : bond 0.00217 ( 8) SS BOND : angle 0.67570 ( 16) covalent geometry : bond 0.00419 (17300) covalent geometry : angle 0.63968 (23595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 4.024 Fit side-chains REVERT: A 90 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8684 (pm20) REVERT: A 141 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7854 (mpt180) REVERT: A 165 GLU cc_start: 0.8675 (tt0) cc_final: 0.8454 (tp30) REVERT: A 244 TYR cc_start: 0.8193 (p90) cc_final: 0.7689 (p90) REVERT: A 306 PHE cc_start: 0.8008 (t80) cc_final: 0.7549 (t80) REVERT: B 265 ASN cc_start: 0.8447 (t0) cc_final: 0.8198 (t0) REVERT: B 268 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8607 (tm) REVERT: C 141 ARG cc_start: 0.8733 (mtt90) cc_final: 0.8384 (mtm180) REVERT: C 235 LEU cc_start: 0.8681 (tp) cc_final: 0.8464 (tt) REVERT: C 244 TYR cc_start: 0.8022 (p90) cc_final: 0.7740 (p90) REVERT: C 274 LYS cc_start: 0.8123 (mttt) cc_final: 0.7733 (mmmm) REVERT: C 434 THR cc_start: 0.9116 (m) cc_final: 0.8878 (p) REVERT: D 68 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8891 (tpp80) REVERT: D 227 MET cc_start: 0.7393 (mmt) cc_final: 0.7152 (mmm) REVERT: D 243 ASN cc_start: 0.8462 (t0) cc_final: 0.7934 (t0) REVERT: D 274 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8310 (mmmm) REVERT: E 107 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: E 208 LYS cc_start: 0.8935 (mttm) cc_final: 0.8571 (mtpt) REVERT: E 260 LEU cc_start: 0.8643 (pp) cc_final: 0.8392 (mm) REVERT: E 330 PHE cc_start: 0.7824 (t80) cc_final: 0.7435 (t80) REVERT: K 407 LEU cc_start: 0.8426 (mt) cc_final: 0.8162 (mp) REVERT: K 469 GLU cc_start: 0.8052 (mp0) cc_final: 0.7800 (mp0) REVERT: K 474 LYS cc_start: 0.7272 (mttp) cc_final: 0.7060 (mptp) REVERT: L 1 GLN cc_start: 0.7975 (mp10) cc_final: 0.7508 (mp10) REVERT: L 3 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8515 (mp10) REVERT: L 459 ARG cc_start: 0.7577 (ppt90) cc_final: 0.7340 (ppt90) REVERT: L 460 ASP cc_start: 0.5852 (p0) cc_final: 0.5617 (p0) REVERT: L 469 GLU cc_start: 0.8011 (mp0) cc_final: 0.7693 (mp0) REVERT: L 472 ASN cc_start: 0.8259 (t0) cc_final: 0.7844 (t0) REVERT: L 474 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7503 (mtmm) REVERT: M 454 ARG cc_start: 0.7154 (mtm110) cc_final: 0.6951 (mtp180) outliers start: 68 outliers final: 34 residues processed: 381 average time/residue: 1.4849 time to fit residues: 639.5342 Evaluate side-chains 351 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN C 185 GLN C 265 ASN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.076081 restraints weight = 157303.260| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 5.13 r_work: 0.2719 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17337 Z= 0.148 Angle : 0.635 14.093 23698 Z= 0.313 Chirality : 0.047 0.600 2695 Planarity : 0.004 0.063 2896 Dihedral : 11.566 112.911 2929 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.98 % Allowed : 17.12 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2027 helix: 1.93 (0.20), residues: 595 sheet: 1.40 (0.21), residues: 584 loop : 0.80 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 440 HIS 0.002 0.001 HIS C 191 PHE 0.024 0.002 PHE A 433 TYR 0.024 0.002 TYR C 299 ARG 0.005 0.000 ARG D 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 9) link_NAG-ASN : angle 3.45815 ( 27) link_ALPHA1-6 : bond 0.00892 ( 4) link_ALPHA1-6 : angle 1.79852 ( 12) link_BETA1-4 : bond 0.00245 ( 12) link_BETA1-4 : angle 1.61707 ( 36) link_ALPHA1-3 : bond 0.01008 ( 4) link_ALPHA1-3 : angle 2.03826 ( 12) hydrogen bonds : bond 0.03965 ( 838) hydrogen bonds : angle 4.55862 ( 2660) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.42477 ( 16) covalent geometry : bond 0.00329 (17300) covalent geometry : angle 0.61934 (23595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: A 141 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7844 (mpt180) REVERT: A 165 GLU cc_start: 0.8684 (tt0) cc_final: 0.8472 (tp30) REVERT: A 244 TYR cc_start: 0.8201 (p90) cc_final: 0.7690 (p90) REVERT: A 306 PHE cc_start: 0.8009 (t80) cc_final: 0.7517 (t80) REVERT: C 21 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8275 (mptt) REVERT: C 141 ARG cc_start: 0.8752 (mtt90) cc_final: 0.8415 (mtm180) REVERT: C 235 LEU cc_start: 0.8672 (tp) cc_final: 0.8445 (tt) REVERT: C 244 TYR cc_start: 0.8103 (p90) cc_final: 0.7837 (p90) REVERT: C 274 LYS cc_start: 0.8083 (mttt) cc_final: 0.7689 (mmmm) REVERT: C 301 PHE cc_start: 0.8512 (t80) cc_final: 0.8269 (t80) REVERT: C 305 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8004 (mp) REVERT: C 434 THR cc_start: 0.9106 (m) cc_final: 0.8863 (p) REVERT: D 9 MET cc_start: 0.7307 (ttp) cc_final: 0.7027 (ptt) REVERT: D 215 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8721 (ttpp) REVERT: D 243 ASN cc_start: 0.8428 (t0) cc_final: 0.7842 (t0) REVERT: E 118 LYS cc_start: 0.9238 (mmmm) cc_final: 0.8789 (mtmt) REVERT: E 208 LYS cc_start: 0.8909 (mttm) cc_final: 0.8559 (mtpt) REVERT: E 250 TYR cc_start: 0.6584 (t80) cc_final: 0.6273 (t80) REVERT: E 330 PHE cc_start: 0.7778 (t80) cc_final: 0.7403 (t80) REVERT: K 407 LEU cc_start: 0.8464 (mt) cc_final: 0.8071 (mp) REVERT: K 470 MET cc_start: 0.8049 (mpp) cc_final: 0.7817 (mpp) REVERT: L 1 GLN cc_start: 0.7962 (mp10) cc_final: 0.7565 (mp10) REVERT: L 3 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8555 (mp10) REVERT: L 469 GLU cc_start: 0.8062 (mp0) cc_final: 0.7689 (mp0) REVERT: M 426 GLN cc_start: 0.8199 (tt0) cc_final: 0.7327 (tp40) outliers start: 67 outliers final: 34 residues processed: 367 average time/residue: 1.2374 time to fit residues: 513.3967 Evaluate side-chains 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.075658 restraints weight = 160997.826| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 5.19 r_work: 0.2708 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17337 Z= 0.145 Angle : 0.627 12.407 23698 Z= 0.309 Chirality : 0.046 0.562 2695 Planarity : 0.004 0.060 2896 Dihedral : 11.232 115.620 2929 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.82 % Allowed : 18.07 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2027 helix: 1.95 (0.21), residues: 595 sheet: 1.52 (0.22), residues: 559 loop : 0.65 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 440 HIS 0.002 0.001 HIS B 107 PHE 0.027 0.002 PHE A 433 TYR 0.022 0.002 TYR B 299 ARG 0.004 0.000 ARG D 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 9) link_NAG-ASN : angle 3.22759 ( 27) link_ALPHA1-6 : bond 0.00923 ( 4) link_ALPHA1-6 : angle 1.76264 ( 12) link_BETA1-4 : bond 0.00285 ( 12) link_BETA1-4 : angle 1.61788 ( 36) link_ALPHA1-3 : bond 0.01037 ( 4) link_ALPHA1-3 : angle 2.02676 ( 12) hydrogen bonds : bond 0.03800 ( 838) hydrogen bonds : angle 4.47178 ( 2660) SS BOND : bond 0.00173 ( 8) SS BOND : angle 0.43170 ( 16) covalent geometry : bond 0.00320 (17300) covalent geometry : angle 0.61213 (23595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.7465 (pmm) cc_final: 0.7216 (mmm) REVERT: A 13 LYS cc_start: 0.8599 (mtpp) cc_final: 0.7962 (mttp) REVERT: A 90 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8712 (pm20) REVERT: A 112 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8683 (mmtm) REVERT: A 141 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7956 (mpt180) REVERT: A 244 TYR cc_start: 0.8208 (p90) cc_final: 0.7718 (p90) REVERT: A 306 PHE cc_start: 0.7962 (t80) cc_final: 0.7579 (t80) REVERT: A 426 TRP cc_start: 0.7994 (m-90) cc_final: 0.7475 (m-10) REVERT: C 21 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8302 (mptt) REVERT: C 141 ARG cc_start: 0.8740 (mtt90) cc_final: 0.8455 (mtm180) REVERT: C 235 LEU cc_start: 0.8711 (tp) cc_final: 0.8504 (tt) REVERT: C 244 TYR cc_start: 0.8243 (p90) cc_final: 0.7951 (p90) REVERT: C 274 LYS cc_start: 0.8053 (mttt) cc_final: 0.7606 (mmmm) REVERT: C 305 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7971 (mp) REVERT: C 434 THR cc_start: 0.9133 (m) cc_final: 0.8889 (p) REVERT: D 18 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8512 (mmtm) REVERT: D 215 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8755 (ttpp) REVERT: D 243 ASN cc_start: 0.8508 (t0) cc_final: 0.7883 (t0) REVERT: D 425 ARG cc_start: 0.8150 (ppt170) cc_final: 0.7917 (ppt170) REVERT: E 208 LYS cc_start: 0.8895 (mttm) cc_final: 0.8551 (mtpt) REVERT: E 330 PHE cc_start: 0.7825 (t80) cc_final: 0.7517 (t80) REVERT: K 407 LEU cc_start: 0.8509 (mt) cc_final: 0.8068 (mp) REVERT: K 470 MET cc_start: 0.7809 (mpp) cc_final: 0.7464 (mpp) REVERT: L 3 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8652 (mp10) REVERT: L 459 ARG cc_start: 0.7722 (ppt90) cc_final: 0.7382 (ppt90) REVERT: L 469 GLU cc_start: 0.8112 (mp0) cc_final: 0.7734 (mp0) REVERT: M 426 GLN cc_start: 0.8266 (tt0) cc_final: 0.7403 (tp40) outliers start: 63 outliers final: 37 residues processed: 364 average time/residue: 1.1281 time to fit residues: 465.7391 Evaluate side-chains 357 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 135 optimal weight: 0.0570 chunk 146 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN C 185 GLN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076882 restraints weight = 160507.850| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 5.46 r_work: 0.2718 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17337 Z= 0.121 Angle : 0.622 11.947 23698 Z= 0.305 Chirality : 0.046 0.490 2695 Planarity : 0.003 0.059 2896 Dihedral : 10.922 117.476 2929 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.09 % Allowed : 19.14 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2027 helix: 1.90 (0.21), residues: 595 sheet: 1.53 (0.22), residues: 560 loop : 0.64 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 237 HIS 0.002 0.001 HIS A 267 PHE 0.027 0.001 PHE A 433 TYR 0.021 0.001 TYR B 299 ARG 0.004 0.000 ARG D 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 9) link_NAG-ASN : angle 3.00864 ( 27) link_ALPHA1-6 : bond 0.00989 ( 4) link_ALPHA1-6 : angle 1.71010 ( 12) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 1.47776 ( 36) link_ALPHA1-3 : bond 0.01063 ( 4) link_ALPHA1-3 : angle 1.97062 ( 12) hydrogen bonds : bond 0.03643 ( 838) hydrogen bonds : angle 4.39036 ( 2660) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.29520 ( 16) covalent geometry : bond 0.00266 (17300) covalent geometry : angle 0.60989 (23595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8558 (mtpp) cc_final: 0.7930 (mttp) REVERT: A 90 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: A 112 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8677 (mmtm) REVERT: A 141 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7969 (mpt180) REVERT: A 244 TYR cc_start: 0.8200 (p90) cc_final: 0.7691 (p90) REVERT: A 306 PHE cc_start: 0.8010 (t80) cc_final: 0.7620 (t80) REVERT: A 426 TRP cc_start: 0.7961 (m-90) cc_final: 0.7489 (m-10) REVERT: B 68 ARG cc_start: 0.9102 (ttt180) cc_final: 0.8901 (tpp80) REVERT: C 21 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8333 (mptt) REVERT: C 141 ARG cc_start: 0.8733 (mtt90) cc_final: 0.8449 (mtm180) REVERT: C 235 LEU cc_start: 0.8661 (tp) cc_final: 0.8430 (tt) REVERT: C 244 TYR cc_start: 0.8297 (p90) cc_final: 0.7971 (p90) REVERT: C 274 LYS cc_start: 0.8087 (mttt) cc_final: 0.7570 (mmmm) REVERT: C 305 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7963 (mp) REVERT: C 434 THR cc_start: 0.9142 (m) cc_final: 0.8905 (p) REVERT: D 9 MET cc_start: 0.7243 (ptp) cc_final: 0.7019 (ptt) REVERT: D 18 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8519 (mmtm) REVERT: D 68 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8922 (tpp80) REVERT: D 215 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8698 (ttpp) REVERT: D 243 ASN cc_start: 0.8532 (t0) cc_final: 0.7931 (t0) REVERT: D 425 ARG cc_start: 0.8130 (ppt170) cc_final: 0.7908 (ppt170) REVERT: E 208 LYS cc_start: 0.8894 (mttm) cc_final: 0.8541 (mtpt) REVERT: E 330 PHE cc_start: 0.7764 (t80) cc_final: 0.7470 (t80) REVERT: K 407 LEU cc_start: 0.8507 (mt) cc_final: 0.8079 (mp) REVERT: K 432 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7690 (ttm-80) REVERT: K 433 GLU cc_start: 0.8384 (pt0) cc_final: 0.8130 (pt0) REVERT: K 469 GLU cc_start: 0.8061 (mp0) cc_final: 0.7810 (mp0) REVERT: K 470 MET cc_start: 0.7872 (mpp) cc_final: 0.7641 (mpp) REVERT: L 1 GLN cc_start: 0.7950 (mp10) cc_final: 0.7569 (mp10) REVERT: L 3 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8582 (mp10) REVERT: L 469 GLU cc_start: 0.8073 (mp0) cc_final: 0.7662 (mp0) REVERT: M 426 GLN cc_start: 0.8279 (tt0) cc_final: 0.7400 (tp40) REVERT: M 438 ILE cc_start: 0.9027 (tt) cc_final: 0.8822 (tp) outliers start: 50 outliers final: 24 residues processed: 354 average time/residue: 1.1339 time to fit residues: 452.7285 Evaluate side-chains 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 322 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 64 GLN C 185 GLN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.075613 restraints weight = 151010.961| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.99 r_work: 0.2713 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17337 Z= 0.147 Angle : 0.639 12.546 23698 Z= 0.313 Chirality : 0.046 0.456 2695 Planarity : 0.004 0.062 2896 Dihedral : 10.354 113.914 2929 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.03 % Allowed : 19.25 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2027 helix: 1.86 (0.21), residues: 595 sheet: 1.48 (0.22), residues: 561 loop : 0.61 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 237 HIS 0.003 0.001 HIS E 240 PHE 0.027 0.002 PHE A 433 TYR 0.023 0.002 TYR E 318 ARG 0.003 0.000 ARG D 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 9) link_NAG-ASN : angle 2.92743 ( 27) link_ALPHA1-6 : bond 0.00931 ( 4) link_ALPHA1-6 : angle 1.70129 ( 12) link_BETA1-4 : bond 0.00291 ( 12) link_BETA1-4 : angle 1.59038 ( 36) link_ALPHA1-3 : bond 0.00965 ( 4) link_ALPHA1-3 : angle 2.09714 ( 12) hydrogen bonds : bond 0.03674 ( 838) hydrogen bonds : angle 4.39996 ( 2660) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.46531 ( 16) covalent geometry : bond 0.00329 (17300) covalent geometry : angle 0.62624 (23595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6831 (mmm) cc_final: 0.6470 (tpt) REVERT: A 13 LYS cc_start: 0.8657 (mtpp) cc_final: 0.7996 (mttp) REVERT: A 90 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: A 112 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8643 (mmtm) REVERT: A 141 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7978 (mpt180) REVERT: A 244 TYR cc_start: 0.8179 (p90) cc_final: 0.7800 (p90) REVERT: A 426 TRP cc_start: 0.7990 (m-90) cc_final: 0.7511 (m-10) REVERT: C 13 LYS cc_start: 0.8976 (tttt) cc_final: 0.8750 (tttm) REVERT: C 21 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8375 (mptt) REVERT: C 141 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8449 (mtm180) REVERT: C 235 LEU cc_start: 0.8719 (tp) cc_final: 0.8494 (tt) REVERT: C 244 TYR cc_start: 0.8303 (p90) cc_final: 0.7950 (p90) REVERT: C 274 LYS cc_start: 0.8105 (mttt) cc_final: 0.7608 (mmmm) REVERT: C 305 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 434 THR cc_start: 0.9183 (m) cc_final: 0.8939 (p) REVERT: D 9 MET cc_start: 0.7216 (ptp) cc_final: 0.6916 (ptt) REVERT: D 18 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8520 (mmtm) REVERT: D 68 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8917 (tpp80) REVERT: D 215 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8725 (ttpp) REVERT: D 218 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6468 (mm) REVERT: D 227 MET cc_start: 0.7541 (mmm) cc_final: 0.7296 (mmm) REVERT: D 243 ASN cc_start: 0.8498 (t0) cc_final: 0.7900 (t0) REVERT: D 425 ARG cc_start: 0.8163 (ppt170) cc_final: 0.7928 (ppt170) REVERT: E 118 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8932 (mtmm) REVERT: E 208 LYS cc_start: 0.8900 (mttm) cc_final: 0.8551 (mtpt) REVERT: E 330 PHE cc_start: 0.7791 (t80) cc_final: 0.7488 (t80) REVERT: K 407 LEU cc_start: 0.8416 (mt) cc_final: 0.7995 (mp) REVERT: K 433 GLU cc_start: 0.8422 (pt0) cc_final: 0.8195 (pt0) REVERT: K 469 GLU cc_start: 0.8069 (mp0) cc_final: 0.7790 (mp0) REVERT: K 470 MET cc_start: 0.7685 (mpp) cc_final: 0.7393 (mpp) REVERT: L 3 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8637 (mp10) REVERT: L 469 GLU cc_start: 0.8014 (mp0) cc_final: 0.7617 (mp0) REVERT: M 426 GLN cc_start: 0.8290 (tt0) cc_final: 0.7443 (tp40) REVERT: M 438 ILE cc_start: 0.9052 (tt) cc_final: 0.8847 (tp) outliers start: 49 outliers final: 33 residues processed: 357 average time/residue: 1.1471 time to fit residues: 461.7533 Evaluate side-chains 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 312 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 445 THR Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 224 GLN C 64 GLN C 185 GLN E 147 GLN E 213 GLN K 471 ASN K 504 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.073847 restraints weight = 157124.596| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 5.06 r_work: 0.2673 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17337 Z= 0.194 Angle : 0.664 12.702 23698 Z= 0.331 Chirality : 0.047 0.425 2695 Planarity : 0.004 0.058 2896 Dihedral : 10.141 116.172 2929 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.25 % Allowed : 19.64 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2027 helix: 1.80 (0.21), residues: 595 sheet: 1.27 (0.21), residues: 585 loop : 0.63 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 440 HIS 0.004 0.001 HIS E 240 PHE 0.028 0.002 PHE A 433 TYR 0.024 0.002 TYR A 299 ARG 0.005 0.001 ARG K 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 9) link_NAG-ASN : angle 2.91211 ( 27) link_ALPHA1-6 : bond 0.00850 ( 4) link_ALPHA1-6 : angle 1.68567 ( 12) link_BETA1-4 : bond 0.00304 ( 12) link_BETA1-4 : angle 1.74836 ( 36) link_ALPHA1-3 : bond 0.00887 ( 4) link_ALPHA1-3 : angle 2.21352 ( 12) hydrogen bonds : bond 0.03884 ( 838) hydrogen bonds : angle 4.54166 ( 2660) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.65970 ( 16) covalent geometry : bond 0.00444 (17300) covalent geometry : angle 0.65159 (23595) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8671 (mmtm) REVERT: A 137 MET cc_start: 0.8499 (tpp) cc_final: 0.8201 (ptt) REVERT: A 141 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7990 (mpt180) REVERT: A 244 TYR cc_start: 0.8198 (p90) cc_final: 0.7878 (p90) REVERT: A 426 TRP cc_start: 0.8012 (m-90) cc_final: 0.7524 (m-10) REVERT: C 21 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8417 (mptt) REVERT: C 141 ARG cc_start: 0.8776 (mtt90) cc_final: 0.8484 (mtm180) REVERT: C 235 LEU cc_start: 0.8744 (tp) cc_final: 0.8520 (tt) REVERT: C 244 TYR cc_start: 0.8328 (p90) cc_final: 0.7993 (p90) REVERT: C 274 LYS cc_start: 0.8133 (mttt) cc_final: 0.7670 (mmmm) REVERT: C 305 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8024 (mp) REVERT: C 434 THR cc_start: 0.9121 (m) cc_final: 0.8873 (p) REVERT: D 215 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8742 (ttpp) REVERT: D 218 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6644 (mm) REVERT: D 243 ASN cc_start: 0.8480 (t0) cc_final: 0.7919 (t0) REVERT: D 425 ARG cc_start: 0.8110 (ppt170) cc_final: 0.7878 (ppt170) REVERT: E 118 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8883 (mtmm) REVERT: E 208 LYS cc_start: 0.8936 (mttm) cc_final: 0.8591 (mtpt) REVERT: E 330 PHE cc_start: 0.7823 (t80) cc_final: 0.7525 (t80) REVERT: K 407 LEU cc_start: 0.8387 (mt) cc_final: 0.8002 (mp) REVERT: K 469 GLU cc_start: 0.8147 (mp0) cc_final: 0.7880 (mp0) REVERT: K 470 MET cc_start: 0.7852 (mpp) cc_final: 0.7543 (mpp) REVERT: L 469 GLU cc_start: 0.8071 (mp0) cc_final: 0.7704 (mp0) REVERT: L 470 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7224 (mpt) REVERT: M 408 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7408 (p) REVERT: M 426 GLN cc_start: 0.8338 (tt0) cc_final: 0.7497 (tp40) outliers start: 53 outliers final: 30 residues processed: 372 average time/residue: 1.1115 time to fit residues: 469.4624 Evaluate side-chains 358 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN C 185 GLN C 224 GLN E 147 GLN E 213 GLN K 426 GLN K 471 ASN ** L 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.073946 restraints weight = 161041.970| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.05 r_work: 0.2679 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17337 Z= 0.172 Angle : 0.675 12.856 23698 Z= 0.332 Chirality : 0.047 0.408 2695 Planarity : 0.004 0.063 2896 Dihedral : 9.921 116.999 2929 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.81 % Allowed : 21.27 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2027 helix: 1.74 (0.21), residues: 595 sheet: 1.30 (0.21), residues: 581 loop : 0.63 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 440 HIS 0.003 0.001 HIS E 240 PHE 0.027 0.002 PHE A 433 TYR 0.025 0.002 TYR E 318 ARG 0.006 0.000 ARG K 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 9) link_NAG-ASN : angle 2.75866 ( 27) link_ALPHA1-6 : bond 0.00893 ( 4) link_ALPHA1-6 : angle 1.65114 ( 12) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.66414 ( 36) link_ALPHA1-3 : bond 0.00933 ( 4) link_ALPHA1-3 : angle 2.08770 ( 12) hydrogen bonds : bond 0.03773 ( 838) hydrogen bonds : angle 4.48935 ( 2660) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.47034 ( 16) covalent geometry : bond 0.00390 (17300) covalent geometry : angle 0.66367 (23595) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 349 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8090 (mttp) REVERT: A 112 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8672 (mmtm) REVERT: A 137 MET cc_start: 0.8496 (tpp) cc_final: 0.8196 (ptt) REVERT: A 141 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7988 (mpt180) REVERT: A 244 TYR cc_start: 0.8194 (p90) cc_final: 0.7896 (p90) REVERT: A 426 TRP cc_start: 0.8012 (m-90) cc_final: 0.7523 (m-10) REVERT: C 13 LYS cc_start: 0.8922 (tttt) cc_final: 0.8706 (tttm) REVERT: C 21 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8432 (mptt) REVERT: C 49 MET cc_start: 0.8398 (tmm) cc_final: 0.8195 (pp-130) REVERT: C 141 ARG cc_start: 0.8783 (mtt90) cc_final: 0.8489 (mtm180) REVERT: C 235 LEU cc_start: 0.8765 (tp) cc_final: 0.8535 (tt) REVERT: C 244 TYR cc_start: 0.8372 (p90) cc_final: 0.8076 (p90) REVERT: C 305 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (mp) REVERT: C 434 THR cc_start: 0.9125 (m) cc_final: 0.8877 (p) REVERT: D 182 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7781 (mt-10) REVERT: D 215 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8734 (ttpp) REVERT: D 218 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6663 (mm) REVERT: D 243 ASN cc_start: 0.8506 (t0) cc_final: 0.7902 (t0) REVERT: D 425 ARG cc_start: 0.8184 (ppt170) cc_final: 0.7954 (ppt170) REVERT: E 118 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8890 (mtmm) REVERT: E 173 MET cc_start: 0.8816 (ptp) cc_final: 0.8595 (ptm) REVERT: E 208 LYS cc_start: 0.8929 (mttm) cc_final: 0.8584 (mtpt) REVERT: E 330 PHE cc_start: 0.7842 (t80) cc_final: 0.7543 (t80) REVERT: K 407 LEU cc_start: 0.8312 (mt) cc_final: 0.7939 (mp) REVERT: K 456 THR cc_start: 0.8292 (t) cc_final: 0.8049 (t) REVERT: K 469 GLU cc_start: 0.8182 (mp0) cc_final: 0.7850 (mp0) REVERT: K 470 MET cc_start: 0.7806 (mpp) cc_final: 0.7447 (mpp) REVERT: K 504 GLN cc_start: 0.8268 (mp10) cc_final: 0.7785 (pm20) REVERT: L 469 GLU cc_start: 0.8114 (mp0) cc_final: 0.7717 (mp0) REVERT: M 426 GLN cc_start: 0.8355 (tt0) cc_final: 0.7382 (tp40) outliers start: 45 outliers final: 31 residues processed: 368 average time/residue: 1.1778 time to fit residues: 486.8325 Evaluate side-chains 362 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 328 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 194 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN C 185 GLN E 147 GLN E 213 GLN K 426 GLN K 471 ASN L 414 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.072542 restraints weight = 155118.196| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.98 r_work: 0.2654 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17337 Z= 0.224 Angle : 0.711 13.709 23698 Z= 0.353 Chirality : 0.048 0.396 2695 Planarity : 0.004 0.060 2896 Dihedral : 9.602 116.730 2929 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.58 % Allowed : 21.72 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2027 helix: 1.57 (0.21), residues: 602 sheet: 1.22 (0.21), residues: 583 loop : 0.53 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 440 HIS 0.004 0.001 HIS B 107 PHE 0.028 0.002 PHE A 433 TYR 0.027 0.002 TYR E 318 ARG 0.005 0.001 ARG K 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 9) link_NAG-ASN : angle 2.81510 ( 27) link_ALPHA1-6 : bond 0.00790 ( 4) link_ALPHA1-6 : angle 1.65947 ( 12) link_BETA1-4 : bond 0.00366 ( 12) link_BETA1-4 : angle 1.85691 ( 36) link_ALPHA1-3 : bond 0.00864 ( 4) link_ALPHA1-3 : angle 2.25844 ( 12) hydrogen bonds : bond 0.03974 ( 838) hydrogen bonds : angle 4.62509 ( 2660) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.70181 ( 16) covalent geometry : bond 0.00514 (17300) covalent geometry : angle 0.69883 (23595) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 348 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8122 (mttp) REVERT: A 112 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8645 (mmtm) REVERT: A 137 MET cc_start: 0.8475 (tpp) cc_final: 0.8223 (ptt) REVERT: A 141 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8034 (mpt180) REVERT: A 426 TRP cc_start: 0.8067 (m-90) cc_final: 0.7518 (m-10) REVERT: C 49 MET cc_start: 0.8421 (tmm) cc_final: 0.8209 (pp-130) REVERT: C 141 ARG cc_start: 0.8770 (mtt90) cc_final: 0.8469 (mtm180) REVERT: C 235 LEU cc_start: 0.8784 (tp) cc_final: 0.8567 (tt) REVERT: C 244 TYR cc_start: 0.8387 (p90) cc_final: 0.8112 (p90) REVERT: C 305 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 434 THR cc_start: 0.9130 (m) cc_final: 0.8882 (p) REVERT: D 182 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7941 (mp0) REVERT: D 215 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8734 (ttpp) REVERT: D 218 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6828 (mm) REVERT: D 243 ASN cc_start: 0.8505 (t0) cc_final: 0.7900 (t0) REVERT: D 425 ARG cc_start: 0.8147 (ppt170) cc_final: 0.7918 (ppt170) REVERT: E 118 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8896 (mtmm) REVERT: E 173 MET cc_start: 0.8892 (ptp) cc_final: 0.8629 (ptm) REVERT: E 208 LYS cc_start: 0.8930 (mttm) cc_final: 0.8585 (mtpt) REVERT: E 330 PHE cc_start: 0.7900 (t80) cc_final: 0.7605 (t80) REVERT: K 407 LEU cc_start: 0.8340 (mt) cc_final: 0.8065 (mp) REVERT: K 469 GLU cc_start: 0.8230 (mp0) cc_final: 0.7916 (mp0) REVERT: K 470 MET cc_start: 0.7845 (mpp) cc_final: 0.7499 (mpp) REVERT: K 504 GLN cc_start: 0.8406 (mp10) cc_final: 0.7964 (pm20) REVERT: L 1 GLN cc_start: 0.8042 (mp10) cc_final: 0.7737 (pm20) REVERT: L 469 GLU cc_start: 0.8218 (mp0) cc_final: 0.7832 (mp0) REVERT: L 470 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7180 (mpt) REVERT: M 466 VAL cc_start: 0.8325 (t) cc_final: 0.7923 (p) outliers start: 41 outliers final: 29 residues processed: 366 average time/residue: 1.1727 time to fit residues: 483.5711 Evaluate side-chains 361 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN C 64 GLN C 185 GLN E 147 GLN E 213 GLN K 426 GLN K 471 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.074785 restraints weight = 154441.915| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 5.02 r_work: 0.2699 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17337 Z= 0.134 Angle : 0.673 13.843 23698 Z= 0.330 Chirality : 0.046 0.375 2695 Planarity : 0.004 0.058 2896 Dihedral : 9.089 112.782 2929 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.36 % Allowed : 22.56 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2027 helix: 1.65 (0.21), residues: 595 sheet: 1.30 (0.21), residues: 574 loop : 0.65 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 440 HIS 0.004 0.001 HIS D 267 PHE 0.027 0.002 PHE A 433 TYR 0.023 0.002 TYR E 318 ARG 0.011 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 9) link_NAG-ASN : angle 2.46425 ( 27) link_ALPHA1-6 : bond 0.00962 ( 4) link_ALPHA1-6 : angle 1.56975 ( 12) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 1.51222 ( 36) link_ALPHA1-3 : bond 0.01057 ( 4) link_ALPHA1-3 : angle 1.92038 ( 12) hydrogen bonds : bond 0.03664 ( 838) hydrogen bonds : angle 4.45337 ( 2660) SS BOND : bond 0.00145 ( 8) SS BOND : angle 0.41174 ( 16) covalent geometry : bond 0.00300 (17300) covalent geometry : angle 0.66466 (23595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15932.67 seconds wall clock time: 276 minutes 32.62 seconds (16592.62 seconds total)