Starting phenix.real_space_refine on Sat Jun 14 13:21:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnc_14074/06_2025/7qnc_14074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnc_14074/06_2025/7qnc_14074.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/7qnc_14074/06_2025/7qnc_14074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnc_14074/06_2025/7qnc_14074.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnc_14074/06_2025/7qnc_14074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnc_14074/06_2025/7qnc_14074.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 10316 2.51 5 N 2538 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15861 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2711 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 318} Chain breaks: 1 Chain: "B" Number of atoms: 2732 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: 2703 Chain: "C" Number of atoms: 2767 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: 2665 Chain: "D" Number of atoms: 2709 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: 2730 Chain: "E" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Chain: "F" 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: "G" 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: 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: "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: "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: "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: "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: "J" 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: "A" 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 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'D10': 1, 'EI7': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'D10': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'D10': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'EI7': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ATYR B 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 66 " occ=0.50 residue: pdb=" N AMET C 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET C 40 " 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 AILE C 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE C 164 " 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 ALEU C 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 214 " occ=0.50 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 residue: pdb=" N HSM C 503 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 503 " occ=0.70 residue: pdb=" N HSM D 503 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 503 " occ=0.70 Time building chain proxies: 16.74, per 1000 atoms: 1.06 Number of scatterers: 15861 At special positions: 0 Unit cell: (117.376, 120.064, 138.88, 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 2915 8.00 N 2538 7.00 C 10316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " 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 F 409 " - pdb=" SG CYS F 483 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 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 H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG B 502 " - " ASN B 8 " " NAG C 502 " - " ASN C 8 " " NAG D 502 " - " ASN D 8 " " NAG E 501 " - " ASN E 65 " " NAG E 503 " - " ASN E 103 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 2.7 seconds 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 37.6% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.614A pdb=" N VAL A 124 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 4.504A pdb=" N ASP A 178 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 263 through 280 removed outlier: 4.050A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.556A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 349 Processing helix chain 'A' and resid 516 through 544 removed outlier: 3.747A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.877A pdb=" N LYS A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) 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 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 Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.577A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 279 through 307 Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.720A 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 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 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.577A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 423 through 447 removed outlier: 3.719A 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 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 Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.577A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 246 through 270 Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 423 through 447 removed outlier: 3.719A 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 43 through 49 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.788A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.718A pdb=" N GLU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Proline residue: E 257 - end of helix removed outlier: 4.061A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 300 removed outlier: 3.555A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER E 300 " --> pdb=" O SER E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 335 Processing helix chain 'E' and resid 425 through 450 removed outlier: 3.719A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Proline residue: E 436 - end of helix Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'G' and resid 449 through 452 Processing helix chain 'G' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.345A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.338A pdb=" N GLY A 137 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A 171 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.329A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.264A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.475A 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: 6.719A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.475A 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: 3.580A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.262A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.476A 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: 6.721A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.476A 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: 3.579A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.264A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.476A 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: 6.720A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.476A 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: 3.580A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.814A 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: 3.516A pdb=" N SER E 155 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.218A 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: 3.516A pdb=" N SER E 155 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU E 84 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE E 78 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 90 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL E 72 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS E 92 " --> pdb=" O LEU E 70 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU E 70 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER E 94 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU E 68 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ARG E 96 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL E 66 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.076A 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: 3.985A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.797A pdb=" N GLY F 10 " --> pdb=" O GLN F 507 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 509 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.797A pdb=" N GLY F 10 " --> pdb=" O GLN F 507 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 509 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR F 501 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.796A pdb=" N GLY G 10 " --> pdb=" O GLN G 507 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 509 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 420 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG G 425 " --> pdb=" O PHE G 434 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE G 434 " --> pdb=" O ARG G 425 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.796A pdb=" N GLY G 10 " --> pdb=" O GLN G 507 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 509 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR G 501 " --> pdb=" O ALA G 485 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2552 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: 7.54 Time building geometry restraints manager: 7.62 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: 4797 1.34 - 1.46: 4329 1.46 - 1.58: 7003 1.58 - 1.69: 0 1.69 - 1.81: 161 Bond restraints: 16290 Sorted by residual: bond pdb=" N EI7 E 502 " pdb=" C EI7 E 502 " ideal model delta sigma weight residual 1.388 1.458 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N EI7 B 503 " pdb=" C EI7 B 503 " ideal model delta sigma weight residual 1.388 1.457 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C EI7 E 502 " pdb=" C2 EI7 E 502 " ideal model delta sigma weight residual 1.446 1.478 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C EI7 B 503 " pdb=" C2 EI7 B 503 " ideal model delta sigma weight residual 1.446 1.476 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 16285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 21573 1.60 - 3.19: 476 3.19 - 4.79: 80 4.79 - 6.39: 26 6.39 - 7.99: 3 Bond angle restraints: 22158 Sorted by residual: angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 113.86 7.99 1.19e+00 7.06e-01 4.50e+01 angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 113.89 7.96 1.19e+00 7.06e-01 4.48e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 113.94 7.91 1.19e+00 7.06e-01 4.42e+01 angle pdb=" N ILE B 305 " pdb=" CA ILE B 305 " pdb=" C ILE B 305 " ideal model delta sigma weight residual 113.42 107.89 5.53 1.17e+00 7.31e-01 2.24e+01 angle pdb=" N ILE C 305 " pdb=" CA ILE C 305 " pdb=" C ILE C 305 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9590 21.78 - 43.56: 292 43.56 - 65.34: 34 65.34 - 87.11: 34 87.11 - 108.89: 19 Dihedral angle restraints: 9969 sinusoidal: 4362 harmonic: 5607 Sorted by residual: dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2334 0.084 - 0.167: 199 0.167 - 0.251: 8 0.251 - 0.335: 5 0.335 - 0.418: 2 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.39e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.28e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.25e+01 ... (remaining 2545 not shown) Planarity restraints: 2719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 8 " 0.035 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN B 8 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 8 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 8 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " -0.037 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" CG ASN B 149 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.057 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 8 " 0.029 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" CG ASN C 8 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 8 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 8 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG C 502 " 0.037 2.00e-02 2.50e+03 ... (remaining 2716 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3941 2.80 - 3.33: 14468 3.33 - 3.85: 27253 3.85 - 4.38: 33104 4.38 - 4.90: 55430 Nonbonded interactions: 134196 Sorted by model distance: nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.276 3.120 nonbonded pdb=" NE ARG A 118 " pdb=" OD2 ASP B 163 " model vdw 2.283 3.120 nonbonded pdb=" O PHE E 439 " pdb=" ND2 ASN E 443 " model vdw 2.288 3.120 nonbonded pdb=" O ALA E 52 " pdb=" NH1 ARG E 99 " model vdw 2.326 3.120 nonbonded pdb=" OG SER A 232 " pdb=" OG1 THR A 247 " model vdw 2.328 3.040 ... (remaining 134191 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 'B' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) selection = (chain 'C' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) selection = (chain 'D' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'a' } ncs_group { reference = 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=0.99 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: 64.690 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: 27.590 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 52.630 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:18.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 0.071 16329 Z= 0.155 Angle : 0.601 9.017 22268 Z= 0.309 Chirality : 0.046 0.418 2548 Planarity : 0.005 0.057 2706 Dihedral : 12.798 108.892 6368 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.48 % Allowed : 3.29 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1889 helix: 0.80 (0.20), residues: 570 sheet: 0.99 (0.23), residues: 501 loop : 0.40 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 440 HIS 0.002 0.001 HIS E 92 PHE 0.019 0.001 PHE C 221 TYR 0.023 0.004 TYR B 157 ARG 0.014 0.002 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.03453 ( 13) link_NAG-ASN : angle 3.40303 ( 39) link_ALPHA1-6 : bond 0.00079 ( 4) link_ALPHA1-6 : angle 0.47613 ( 12) link_BETA1-4 : bond 0.00184 ( 11) link_BETA1-4 : angle 1.15365 ( 33) link_ALPHA1-3 : bond 0.00040 ( 4) link_ALPHA1-3 : angle 0.46341 ( 12) hydrogen bonds : bond 0.21645 ( 816) hydrogen bonds : angle 7.34191 ( 2552) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.61942 ( 14) covalent geometry : bond 0.00310 (16290) covalent geometry : angle 0.58275 (22158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 423 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8105 (pt0) cc_final: 0.7848 (pm20) REVERT: A 345 ASN cc_start: 0.8597 (m110) cc_final: 0.8186 (m110) REVERT: B 244 TYR cc_start: 0.8256 (p90) cc_final: 0.7693 (p90) REVERT: B 265 ASN cc_start: 0.8836 (t0) cc_final: 0.8596 (t0) REVERT: B 283 MET cc_start: 0.8669 (mmm) cc_final: 0.8409 (mmm) REVERT: B 425 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8039 (mpt180) REVERT: C 306 PHE cc_start: 0.8020 (t80) cc_final: 0.7102 (t80) REVERT: D 9 MET cc_start: 0.8261 (mtp) cc_final: 0.7816 (ttm) REVERT: E 142 LYS cc_start: 0.9019 (mttt) cc_final: 0.8775 (mttp) REVERT: E 170 LYS cc_start: 0.8774 (mttt) cc_final: 0.8518 (mtpm) REVERT: E 219 TYR cc_start: 0.8699 (p90) cc_final: 0.8373 (p90) REVERT: E 308 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8654 (mtmm) REVERT: F 407 LEU cc_start: 0.8932 (mt) cc_final: 0.8666 (mm) REVERT: F 415 THR cc_start: 0.9051 (p) cc_final: 0.8687 (m) REVERT: F 426 GLN cc_start: 0.8536 (tt0) cc_final: 0.8075 (tp-100) REVERT: F 465 THR cc_start: 0.8817 (m) cc_final: 0.8022 (m) REVERT: F 470 MET cc_start: 0.8282 (mtm) cc_final: 0.7943 (mtp) REVERT: F 481 TYR cc_start: 0.7497 (m-80) cc_final: 0.7173 (m-80) REVERT: G 412 SER cc_start: 0.9108 (p) cc_final: 0.8501 (p) REVERT: G 456 THR cc_start: 0.7957 (p) cc_final: 0.7645 (m) REVERT: G 457 ILE cc_start: 0.9018 (mt) cc_final: 0.8746 (mt) REVERT: G 458 SER cc_start: 0.8591 (t) cc_final: 0.8279 (t) REVERT: G 466 VAL cc_start: 0.8688 (t) cc_final: 0.8414 (m) REVERT: G 490 SER cc_start: 0.8873 (m) cc_final: 0.8573 (m) outliers start: 7 outliers final: 2 residues processed: 427 average time/residue: 1.5113 time to fit residues: 710.4782 Evaluate side-chains 248 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.0050 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 41 ASN B B 148 GLN C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 43 ASN E 77 HIS E 200 GLN E 227 ASN E 233 GLN E 253 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.059283 restraints weight = 116001.438| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 5.01 r_work: 0.2559 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16329 Z= 0.211 Angle : 0.681 8.734 22268 Z= 0.348 Chirality : 0.046 0.260 2548 Planarity : 0.004 0.039 2706 Dihedral : 9.151 80.687 2847 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.64 % Allowed : 13.38 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.79 (0.19), residues: 1889 helix: 2.22 (0.21), residues: 570 sheet: 1.01 (0.23), residues: 499 loop : 0.69 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 426 HIS 0.009 0.001 HIS B 267 PHE 0.024 0.002 PHE D 221 TYR 0.026 0.002 TYR C 299 ARG 0.009 0.001 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.01047 ( 13) link_NAG-ASN : angle 2.21913 ( 39) link_ALPHA1-6 : bond 0.00607 ( 4) link_ALPHA1-6 : angle 1.61749 ( 12) link_BETA1-4 : bond 0.00491 ( 11) link_BETA1-4 : angle 1.77783 ( 33) link_ALPHA1-3 : bond 0.00782 ( 4) link_ALPHA1-3 : angle 2.27252 ( 12) hydrogen bonds : bond 0.05486 ( 816) hydrogen bonds : angle 5.02886 ( 2552) SS BOND : bond 0.00283 ( 7) SS BOND : angle 0.75447 ( 14) covalent geometry : bond 0.00480 (16290) covalent geometry : angle 0.66914 (22158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: A 92 GLU cc_start: 0.9021 (pt0) cc_final: 0.8300 (pm20) REVERT: A 345 ASN cc_start: 0.8413 (m110) cc_final: 0.7919 (m110) REVERT: B 244 TYR cc_start: 0.8592 (p90) cc_final: 0.8202 (p90) REVERT: B 265 ASN cc_start: 0.8942 (t0) cc_final: 0.8740 (t0) REVERT: B 283 MET cc_start: 0.8846 (mmm) cc_final: 0.8612 (mmm) REVERT: B 425 ARG cc_start: 0.8898 (ttt180) cc_final: 0.8084 (mpt180) REVERT: C 306 PHE cc_start: 0.8449 (t80) cc_final: 0.7854 (t80) REVERT: D 9 MET cc_start: 0.8100 (mtp) cc_final: 0.7479 (ttm) REVERT: D 220 TYR cc_start: 0.8621 (t80) cc_final: 0.8386 (t80) REVERT: D 223 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8709 (pp) REVERT: D 244 TYR cc_start: 0.8774 (p90) cc_final: 0.8507 (p90) REVERT: D 286 MET cc_start: 0.8828 (mtm) cc_final: 0.8583 (mtm) REVERT: D 426 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: E 142 LYS cc_start: 0.9439 (mttt) cc_final: 0.9220 (mttp) REVERT: E 147 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: E 170 LYS cc_start: 0.8757 (mttt) cc_final: 0.8555 (mtpm) REVERT: E 179 MET cc_start: 0.8881 (mpp) cc_final: 0.8558 (mpp) REVERT: E 210 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: E 256 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8213 (mmm) REVERT: E 308 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8707 (mtmp) REVERT: F 1 GLN cc_start: 0.8672 (mp10) cc_final: 0.8390 (mp10) REVERT: F 407 LEU cc_start: 0.9180 (mt) cc_final: 0.8788 (mm) REVERT: F 415 THR cc_start: 0.9223 (p) cc_final: 0.8845 (m) REVERT: F 426 GLN cc_start: 0.9079 (tt0) cc_final: 0.8792 (tt0) REVERT: F 433 GLU cc_start: 0.8961 (pt0) cc_final: 0.8656 (pt0) REVERT: F 459 ARG cc_start: 0.8116 (pmt170) cc_final: 0.7872 (ppt170) REVERT: F 470 MET cc_start: 0.8696 (mtm) cc_final: 0.8257 (mtt) REVERT: F 481 TYR cc_start: 0.7938 (m-80) cc_final: 0.7544 (m-80) REVERT: G 469 GLU cc_start: 0.7528 (mp0) cc_final: 0.7168 (mp0) outliers start: 59 outliers final: 20 residues processed: 301 average time/residue: 1.0938 time to fit residues: 369.3744 Evaluate side-chains 272 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 133 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 77 HIS E 200 GLN E 227 ASN E 240 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.060007 restraints weight = 125708.508| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 5.16 r_work: 0.2568 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 16329 Z= 0.148 Angle : 0.622 10.994 22268 Z= 0.316 Chirality : 0.045 0.254 2548 Planarity : 0.004 0.049 2706 Dihedral : 8.280 71.638 2847 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.35 % Allowed : 14.76 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.84 (0.20), residues: 1889 helix: 2.25 (0.21), residues: 582 sheet: 0.92 (0.23), residues: 517 loop : 0.80 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 426 HIS 0.005 0.001 HIS E 240 PHE 0.018 0.002 PHE D 221 TYR 0.029 0.002 TYR C 299 ARG 0.005 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 13) link_NAG-ASN : angle 1.80004 ( 39) link_ALPHA1-6 : bond 0.00724 ( 4) link_ALPHA1-6 : angle 1.64592 ( 12) link_BETA1-4 : bond 0.00370 ( 11) link_BETA1-4 : angle 1.50940 ( 33) link_ALPHA1-3 : bond 0.01045 ( 4) link_ALPHA1-3 : angle 1.75945 ( 12) hydrogen bonds : bond 0.04489 ( 816) hydrogen bonds : angle 4.63821 ( 2552) SS BOND : bond 0.00244 ( 7) SS BOND : angle 0.41073 ( 14) covalent geometry : bond 0.00332 (16290) covalent geometry : angle 0.61405 (22158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8883 (mp0) REVERT: A 92 GLU cc_start: 0.8986 (pt0) cc_final: 0.8280 (pm20) REVERT: A 131 ASP cc_start: 0.9148 (p0) cc_final: 0.8629 (p0) REVERT: A 345 ASN cc_start: 0.8368 (m110) cc_final: 0.7906 (m110) REVERT: B 49 MET cc_start: 0.8477 (tmm) cc_final: 0.8102 (pp-130) REVERT: B 190 GLU cc_start: 0.8949 (tt0) cc_final: 0.8709 (pt0) REVERT: B 223 LEU cc_start: 0.9515 (tp) cc_final: 0.9269 (pp) REVERT: B 244 TYR cc_start: 0.8575 (p90) cc_final: 0.8235 (p90) REVERT: B 425 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8106 (mpt180) REVERT: B 440 LEU cc_start: 0.8974 (tt) cc_final: 0.8748 (tp) REVERT: C 286 MET cc_start: 0.8261 (mmm) cc_final: 0.7656 (mtm) REVERT: C 306 PHE cc_start: 0.8379 (t80) cc_final: 0.7705 (t80) REVERT: D 9 MET cc_start: 0.8169 (mtp) cc_final: 0.7693 (ttm) REVERT: D 95 ASP cc_start: 0.9076 (p0) cc_final: 0.8695 (p0) REVERT: D 220 TYR cc_start: 0.8683 (t80) cc_final: 0.8339 (t80) REVERT: D 244 TYR cc_start: 0.8623 (p90) cc_final: 0.8395 (p90) REVERT: D 286 MET cc_start: 0.8880 (mtm) cc_final: 0.8656 (mtm) REVERT: D 426 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: E 142 LYS cc_start: 0.9420 (mttt) cc_final: 0.9204 (mttp) REVERT: E 147 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: E 179 MET cc_start: 0.8817 (mpp) cc_final: 0.8474 (mpp) REVERT: E 210 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: E 308 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8466 (mtmp) REVERT: F 407 LEU cc_start: 0.9142 (mt) cc_final: 0.8792 (mm) REVERT: F 415 THR cc_start: 0.9248 (p) cc_final: 0.8851 (m) REVERT: F 426 GLN cc_start: 0.9092 (tt0) cc_final: 0.8795 (tt0) REVERT: F 433 GLU cc_start: 0.8973 (pt0) cc_final: 0.8672 (pt0) REVERT: F 459 ARG cc_start: 0.8068 (pmt170) cc_final: 0.7807 (ppt170) REVERT: F 472 ASN cc_start: 0.8407 (m-40) cc_final: 0.8199 (m-40) REVERT: F 481 TYR cc_start: 0.8139 (m-80) cc_final: 0.7840 (m-80) REVERT: G 407 LEU cc_start: 0.8908 (mt) cc_final: 0.8667 (mp) REVERT: G 440 TRP cc_start: 0.8632 (m100) cc_final: 0.8281 (m100) REVERT: G 460 ASP cc_start: 0.6382 (p0) cc_final: 0.6087 (p0) REVERT: G 469 GLU cc_start: 0.8152 (mp0) cc_final: 0.7735 (mp0) REVERT: G 504 GLN cc_start: 0.8612 (pm20) cc_final: 0.8382 (pm20) outliers start: 54 outliers final: 16 residues processed: 311 average time/residue: 1.2593 time to fit residues: 434.7920 Evaluate side-chains 281 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 441 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 165 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS C 64 GLN A C 243 ASN C 265 ASN E 77 HIS E 213 GLN E 227 ASN G 414 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.054266 restraints weight = 128183.049| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 5.10 r_work: 0.2453 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 16329 Z= 0.350 Angle : 0.747 10.737 22268 Z= 0.380 Chirality : 0.050 0.249 2548 Planarity : 0.004 0.046 2706 Dihedral : 8.494 75.044 2847 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.06 % Allowed : 15.65 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.60 (0.20), residues: 1889 helix: 2.20 (0.21), residues: 576 sheet: 0.76 (0.23), residues: 526 loop : 0.54 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 426 HIS 0.006 0.002 HIS E 135 PHE 0.023 0.002 PHE D 221 TYR 0.037 0.002 TYR C 299 ARG 0.006 0.001 ARG B 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 13) link_NAG-ASN : angle 2.34276 ( 39) link_ALPHA1-6 : bond 0.00511 ( 4) link_ALPHA1-6 : angle 1.81120 ( 12) link_BETA1-4 : bond 0.00591 ( 11) link_BETA1-4 : angle 2.09130 ( 33) link_ALPHA1-3 : bond 0.00718 ( 4) link_ALPHA1-3 : angle 2.14055 ( 12) hydrogen bonds : bond 0.04758 ( 816) hydrogen bonds : angle 4.84252 ( 2552) SS BOND : bond 0.00326 ( 7) SS BOND : angle 0.89949 ( 14) covalent geometry : bond 0.00812 (16290) covalent geometry : angle 0.73441 (22158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.9027 (mp0) REVERT: A 92 GLU cc_start: 0.9013 (pt0) cc_final: 0.8462 (pm20) REVERT: A 155 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8390 (mpp) REVERT: A 345 ASN cc_start: 0.8363 (m110) cc_final: 0.7919 (m110) REVERT: B 49 MET cc_start: 0.8551 (tmm) cc_final: 0.8173 (pp-130) REVERT: B 223 LEU cc_start: 0.9499 (tp) cc_final: 0.9169 (pp) REVERT: B 224 GLN cc_start: 0.9100 (tp40) cc_final: 0.8830 (tp40) REVERT: B 244 TYR cc_start: 0.8626 (p90) cc_final: 0.8366 (p90) REVERT: B 425 ARG cc_start: 0.8884 (ttt180) cc_final: 0.8066 (mpt180) REVERT: C 227 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8726 (tpp) REVERT: C 255 ILE cc_start: 0.9488 (pp) cc_final: 0.9252 (pp) REVERT: C 286 MET cc_start: 0.8255 (mmm) cc_final: 0.7720 (mtm) REVERT: C 306 PHE cc_start: 0.8346 (t80) cc_final: 0.7651 (t80) REVERT: D 9 MET cc_start: 0.8056 (mtp) cc_final: 0.7675 (mpp) REVERT: D 286 MET cc_start: 0.8951 (mtm) cc_final: 0.8690 (mtm) REVERT: D 426 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: E 83 MET cc_start: 0.9382 (mmm) cc_final: 0.9178 (mmm) REVERT: E 142 LYS cc_start: 0.9449 (mttt) cc_final: 0.9241 (mttp) REVERT: E 170 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8620 (mttm) REVERT: E 179 MET cc_start: 0.8985 (mpp) cc_final: 0.8640 (mpp) REVERT: E 308 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8645 (mtmp) REVERT: F 407 LEU cc_start: 0.9374 (mt) cc_final: 0.9033 (mm) REVERT: F 426 GLN cc_start: 0.9143 (tt0) cc_final: 0.8907 (tt0) REVERT: F 459 ARG cc_start: 0.8255 (pmt170) cc_final: 0.8016 (ppt170) REVERT: F 470 MET cc_start: 0.8655 (mtp) cc_final: 0.8276 (mtm) REVERT: F 472 ASN cc_start: 0.8935 (m-40) cc_final: 0.8716 (m-40) REVERT: G 407 LEU cc_start: 0.9011 (mt) cc_final: 0.8721 (mp) REVERT: G 440 TRP cc_start: 0.8805 (m100) cc_final: 0.8513 (m100) REVERT: G 469 GLU cc_start: 0.8195 (mp0) cc_final: 0.7698 (mp0) REVERT: G 470 MET cc_start: 0.8737 (mtm) cc_final: 0.7666 (mtm) REVERT: G 476 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8730 (tp30) REVERT: G 504 GLN cc_start: 0.8503 (pm20) cc_final: 0.8259 (pm20) outliers start: 67 outliers final: 21 residues processed: 287 average time/residue: 1.2437 time to fit residues: 397.9598 Evaluate side-chains 272 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 441 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN D 265 ASN E 43 ASN E 77 HIS E 213 GLN E 227 ASN G 414 HIS ** G 504 GLN ** 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 = 0.3323 r_free = 0.3323 target = 0.085077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.056471 restraints weight = 117817.905| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 4.97 r_work: 0.2507 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16329 Z= 0.177 Angle : 0.640 9.376 22268 Z= 0.324 Chirality : 0.046 0.244 2548 Planarity : 0.003 0.037 2706 Dihedral : 7.732 68.940 2847 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.35 % Allowed : 16.37 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.60 (0.20), residues: 1889 helix: 2.27 (0.21), residues: 575 sheet: 0.69 (0.23), residues: 515 loop : 0.54 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 426 HIS 0.003 0.001 HIS E 240 PHE 0.019 0.002 PHE D 221 TYR 0.028 0.002 TYR C 299 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 13) link_NAG-ASN : angle 1.90457 ( 39) link_ALPHA1-6 : bond 0.00802 ( 4) link_ALPHA1-6 : angle 1.79140 ( 12) link_BETA1-4 : bond 0.00364 ( 11) link_BETA1-4 : angle 1.61593 ( 33) link_ALPHA1-3 : bond 0.00888 ( 4) link_ALPHA1-3 : angle 1.72797 ( 12) hydrogen bonds : bond 0.04125 ( 816) hydrogen bonds : angle 4.59880 ( 2552) SS BOND : bond 0.00162 ( 7) SS BOND : angle 0.40751 ( 14) covalent geometry : bond 0.00402 (16290) covalent geometry : angle 0.63034 (22158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.9049 (mp0) REVERT: A 92 GLU cc_start: 0.9009 (pt0) cc_final: 0.8424 (pm20) REVERT: A 155 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8361 (mpp) REVERT: A 319 MET cc_start: 0.9219 (ttp) cc_final: 0.8960 (ttm) REVERT: A 345 ASN cc_start: 0.8345 (m110) cc_final: 0.7896 (m110) REVERT: B 49 MET cc_start: 0.8610 (tmm) cc_final: 0.8206 (pp-130) REVERT: B 223 LEU cc_start: 0.9482 (tp) cc_final: 0.9179 (pp) REVERT: B 224 GLN cc_start: 0.9117 (tp40) cc_final: 0.8881 (tp40) REVERT: B 244 TYR cc_start: 0.8603 (p90) cc_final: 0.8352 (p90) REVERT: B 425 ARG cc_start: 0.8841 (ttt180) cc_final: 0.7998 (mpt180) REVERT: C 227 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8680 (tpp) REVERT: C 255 ILE cc_start: 0.9459 (pp) cc_final: 0.9210 (pp) REVERT: C 286 MET cc_start: 0.8271 (mmm) cc_final: 0.7682 (mtm) REVERT: C 301 PHE cc_start: 0.8857 (t80) cc_final: 0.8330 (t80) REVERT: C 306 PHE cc_start: 0.8288 (t80) cc_final: 0.7545 (t80) REVERT: D 9 MET cc_start: 0.8062 (mtp) cc_final: 0.7704 (mpp) REVERT: D 95 ASP cc_start: 0.9159 (p0) cc_final: 0.8732 (p0) REVERT: D 286 MET cc_start: 0.8922 (mtm) cc_final: 0.8619 (mtm) REVERT: D 426 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7981 (m-10) REVERT: E 142 LYS cc_start: 0.9412 (mttt) cc_final: 0.9202 (mttp) REVERT: E 147 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: E 179 MET cc_start: 0.8924 (mpp) cc_final: 0.8598 (mpp) REVERT: E 226 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7110 (tmt) REVERT: E 229 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8403 (mmmt) REVERT: E 308 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8523 (mtmp) REVERT: F 407 LEU cc_start: 0.9353 (mt) cc_final: 0.8987 (mm) REVERT: F 426 GLN cc_start: 0.9148 (tt0) cc_final: 0.8907 (tt0) REVERT: F 458 SER cc_start: 0.9026 (t) cc_final: 0.8617 (p) REVERT: F 459 ARG cc_start: 0.8159 (pmt170) cc_final: 0.7787 (pmt170) REVERT: F 469 GLU cc_start: 0.8478 (mp0) cc_final: 0.8097 (mp0) REVERT: F 470 MET cc_start: 0.8846 (mtp) cc_final: 0.8511 (mtm) REVERT: F 472 ASN cc_start: 0.8882 (m-40) cc_final: 0.8648 (m-40) REVERT: G 1 GLN cc_start: 0.8387 (mp10) cc_final: 0.7803 (pm20) REVERT: G 433 GLU cc_start: 0.8418 (pp20) cc_final: 0.8169 (pp20) REVERT: G 440 TRP cc_start: 0.8735 (m100) cc_final: 0.8386 (m100) REVERT: G 469 GLU cc_start: 0.8195 (mp0) cc_final: 0.7627 (mp0) REVERT: G 470 MET cc_start: 0.8646 (mtm) cc_final: 0.8276 (mtp) REVERT: G 472 ASN cc_start: 0.9038 (m-40) cc_final: 0.8156 (t0) REVERT: G 476 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8679 (tp30) REVERT: G 478 THR cc_start: 0.8852 (m) cc_final: 0.8593 (p) REVERT: G 504 GLN cc_start: 0.8515 (pm20) cc_final: 0.8288 (pm20) outliers start: 55 outliers final: 20 residues processed: 289 average time/residue: 1.2242 time to fit residues: 392.8532 Evaluate side-chains 275 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 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 225 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN E 77 HIS E 227 ASN E 253 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.056565 restraints weight = 110414.932| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.79 r_work: 0.2517 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16329 Z= 0.183 Angle : 0.642 10.071 22268 Z= 0.323 Chirality : 0.046 0.303 2548 Planarity : 0.004 0.036 2706 Dihedral : 7.353 66.600 2847 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.35 % Allowed : 16.73 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.60 (0.20), residues: 1889 helix: 2.28 (0.21), residues: 575 sheet: 0.71 (0.23), residues: 515 loop : 0.52 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 426 HIS 0.004 0.001 HIS E 104 PHE 0.017 0.001 PHE D 221 TYR 0.027 0.002 TYR E 318 ARG 0.004 0.000 ARG D 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 13) link_NAG-ASN : angle 2.07633 ( 39) link_ALPHA1-6 : bond 0.00821 ( 4) link_ALPHA1-6 : angle 1.80000 ( 12) link_BETA1-4 : bond 0.00414 ( 11) link_BETA1-4 : angle 1.65097 ( 33) link_ALPHA1-3 : bond 0.00937 ( 4) link_ALPHA1-3 : angle 1.89706 ( 12) hydrogen bonds : bond 0.03993 ( 816) hydrogen bonds : angle 4.51083 ( 2552) SS BOND : bond 0.00165 ( 7) SS BOND : angle 0.42083 ( 14) covalent geometry : bond 0.00417 (16290) covalent geometry : angle 0.63109 (22158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.9022 (mp0) REVERT: A 92 GLU cc_start: 0.8979 (pt0) cc_final: 0.8439 (pm20) REVERT: A 155 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8412 (mpp) REVERT: A 319 MET cc_start: 0.9238 (ttp) cc_final: 0.8991 (ttm) REVERT: A 345 ASN cc_start: 0.8338 (m110) cc_final: 0.7891 (m110) REVERT: B 49 MET cc_start: 0.8683 (tmm) cc_final: 0.8287 (pp-130) REVERT: B 223 LEU cc_start: 0.9485 (tp) cc_final: 0.9191 (pp) REVERT: B 224 GLN cc_start: 0.9105 (tp40) cc_final: 0.8832 (tp40) REVERT: B 244 TYR cc_start: 0.8612 (p90) cc_final: 0.8401 (p90) REVERT: B 286 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7793 (mpp) REVERT: B 425 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8012 (mpt180) REVERT: C 190 GLU cc_start: 0.8864 (tt0) cc_final: 0.8514 (pt0) REVERT: C 244 TYR cc_start: 0.8404 (p90) cc_final: 0.8197 (p90) REVERT: C 255 ILE cc_start: 0.9495 (pp) cc_final: 0.9255 (pp) REVERT: C 274 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8886 (mmmm) REVERT: C 286 MET cc_start: 0.8266 (mmm) cc_final: 0.7711 (mtm) REVERT: C 301 PHE cc_start: 0.8865 (t80) cc_final: 0.8224 (t80) REVERT: D 9 MET cc_start: 0.8038 (mtp) cc_final: 0.7636 (mpp) REVERT: D 95 ASP cc_start: 0.9143 (p0) cc_final: 0.8718 (p0) REVERT: D 286 MET cc_start: 0.8930 (mtm) cc_final: 0.8612 (mtm) REVERT: D 426 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: E 147 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: E 170 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8724 (mttm) REVERT: E 179 MET cc_start: 0.8939 (mpp) cc_final: 0.8644 (mpp) REVERT: E 210 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: E 288 LEU cc_start: 0.8939 (mt) cc_final: 0.8639 (pp) REVERT: E 308 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8513 (mtmp) REVERT: F 407 LEU cc_start: 0.9332 (mt) cc_final: 0.9024 (mt) REVERT: F 458 SER cc_start: 0.9039 (t) cc_final: 0.8658 (p) REVERT: F 459 ARG cc_start: 0.8193 (pmt170) cc_final: 0.7828 (pmt170) REVERT: F 469 GLU cc_start: 0.8581 (mp0) cc_final: 0.8202 (mp0) REVERT: F 470 MET cc_start: 0.8823 (mtp) cc_final: 0.8526 (mtm) REVERT: F 472 ASN cc_start: 0.8886 (m-40) cc_final: 0.8656 (m-40) REVERT: G 407 LEU cc_start: 0.8835 (mp) cc_final: 0.8614 (mt) REVERT: G 433 GLU cc_start: 0.8384 (pp20) cc_final: 0.8096 (pp20) REVERT: G 440 TRP cc_start: 0.8657 (m100) cc_final: 0.8317 (m100) REVERT: G 469 GLU cc_start: 0.8163 (mp0) cc_final: 0.7580 (mp0) REVERT: G 470 MET cc_start: 0.8632 (mtm) cc_final: 0.8192 (mtp) REVERT: G 472 ASN cc_start: 0.9142 (m-40) cc_final: 0.8505 (t0) REVERT: G 474 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7534 (mptm) REVERT: G 478 THR cc_start: 0.8906 (m) cc_final: 0.8676 (p) REVERT: G 504 GLN cc_start: 0.8494 (pm20) cc_final: 0.8281 (pm20) outliers start: 55 outliers final: 23 residues processed: 288 average time/residue: 1.2478 time to fit residues: 400.4523 Evaluate side-chains 282 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN B E 77 HIS E 227 ASN E 253 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.057446 restraints weight = 121897.224| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 5.01 r_work: 0.2512 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 16329 Z= 0.144 Angle : 0.640 11.150 22268 Z= 0.317 Chirality : 0.046 0.333 2548 Planarity : 0.003 0.037 2706 Dihedral : 6.646 61.373 2847 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.29 % Allowed : 17.44 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.64 (0.20), residues: 1889 helix: 2.28 (0.21), residues: 578 sheet: 0.70 (0.23), residues: 519 loop : 0.58 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 PHE 0.020 0.001 PHE A 291 TYR 0.025 0.001 TYR E 318 ARG 0.004 0.000 ARG F 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 13) link_NAG-ASN : angle 1.86450 ( 39) link_ALPHA1-6 : bond 0.00965 ( 4) link_ALPHA1-6 : angle 1.71226 ( 12) link_BETA1-4 : bond 0.00437 ( 11) link_BETA1-4 : angle 1.49047 ( 33) link_ALPHA1-3 : bond 0.01103 ( 4) link_ALPHA1-3 : angle 1.82304 ( 12) hydrogen bonds : bond 0.03763 ( 816) hydrogen bonds : angle 4.39256 ( 2552) SS BOND : bond 0.00132 ( 7) SS BOND : angle 0.32426 ( 14) covalent geometry : bond 0.00330 (16290) covalent geometry : angle 0.63146 (22158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8979 (mp0) REVERT: A 92 GLU cc_start: 0.8999 (pt0) cc_final: 0.8412 (pm20) REVERT: A 131 ASP cc_start: 0.9248 (p0) cc_final: 0.8677 (p0) REVERT: A 155 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8345 (mpp) REVERT: A 175 ARG cc_start: 0.8873 (mmm160) cc_final: 0.8659 (mmm160) REVERT: A 319 MET cc_start: 0.9200 (ttp) cc_final: 0.8979 (ttm) REVERT: A 345 ASN cc_start: 0.8361 (m110) cc_final: 0.7925 (m110) REVERT: B 49 MET cc_start: 0.8639 (tmm) cc_final: 0.8203 (pp-130) REVERT: B 223 LEU cc_start: 0.9490 (tp) cc_final: 0.9193 (pp) REVERT: B 224 GLN cc_start: 0.9031 (tp40) cc_final: 0.8805 (tp40) REVERT: B 244 TYR cc_start: 0.8631 (p90) cc_final: 0.8408 (p90) REVERT: B 286 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7602 (mpp) REVERT: B 425 ARG cc_start: 0.8836 (ttt180) cc_final: 0.7989 (mpt180) REVERT: B 433 PHE cc_start: 0.8579 (t80) cc_final: 0.8351 (t80) REVERT: B 437 LEU cc_start: 0.8673 (tm) cc_final: 0.8292 (mp) REVERT: C 49 MET cc_start: 0.8362 (tmm) cc_final: 0.8055 (ppp) REVERT: C 190 GLU cc_start: 0.8944 (tt0) cc_final: 0.8582 (pt0) REVERT: C 255 ILE cc_start: 0.9415 (pp) cc_final: 0.9190 (pp) REVERT: C 274 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8930 (mmmm) REVERT: C 286 MET cc_start: 0.8153 (mmm) cc_final: 0.7589 (mtm) REVERT: C 301 PHE cc_start: 0.8795 (t80) cc_final: 0.8169 (t80) REVERT: D 9 MET cc_start: 0.8062 (mtp) cc_final: 0.7614 (mpp) REVERT: D 95 ASP cc_start: 0.9105 (p0) cc_final: 0.8680 (p0) REVERT: D 220 TYR cc_start: 0.8622 (t80) cc_final: 0.8350 (t80) REVERT: D 286 MET cc_start: 0.8909 (mtm) cc_final: 0.8594 (mtm) REVERT: D 426 TRP cc_start: 0.8364 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: E 147 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: E 170 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8558 (mttm) REVERT: E 173 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9069 (mpp) REVERT: E 179 MET cc_start: 0.8862 (mpp) cc_final: 0.8512 (mpp) REVERT: E 210 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: E 308 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8323 (mtmp) REVERT: F 407 LEU cc_start: 0.9266 (mt) cc_final: 0.9046 (mt) REVERT: F 458 SER cc_start: 0.9073 (t) cc_final: 0.8693 (p) REVERT: F 459 ARG cc_start: 0.8246 (pmt170) cc_final: 0.7857 (ppt170) REVERT: F 469 GLU cc_start: 0.8687 (mp0) cc_final: 0.8244 (mp0) REVERT: F 470 MET cc_start: 0.8862 (mtp) cc_final: 0.8548 (mtm) REVERT: F 473 LEU cc_start: 0.8790 (tt) cc_final: 0.8282 (mp) REVERT: F 501 TYR cc_start: 0.9070 (m-80) cc_final: 0.8824 (m-80) REVERT: G 1 GLN cc_start: 0.8431 (mp10) cc_final: 0.7998 (pm20) REVERT: G 407 LEU cc_start: 0.8765 (mp) cc_final: 0.8562 (mt) REVERT: G 433 GLU cc_start: 0.8462 (pp20) cc_final: 0.8155 (pp20) REVERT: G 440 TRP cc_start: 0.8577 (m100) cc_final: 0.8254 (m100) REVERT: G 459 ARG cc_start: 0.8421 (ppt90) cc_final: 0.7938 (ptt-90) REVERT: G 469 GLU cc_start: 0.8150 (mp0) cc_final: 0.7543 (mp0) REVERT: G 470 MET cc_start: 0.8598 (mtm) cc_final: 0.8298 (mtp) REVERT: G 472 ASN cc_start: 0.9204 (m-40) cc_final: 0.8572 (t0) REVERT: G 474 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7453 (mptm) REVERT: G 504 GLN cc_start: 0.8483 (pm20) cc_final: 0.8256 (pm20) outliers start: 54 outliers final: 22 residues processed: 289 average time/residue: 1.1516 time to fit residues: 371.5049 Evaluate side-chains 285 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS 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 225 THR Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN E 227 ASN E 253 GLN G 414 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.058744 restraints weight = 101703.993| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 4.61 r_work: 0.2534 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16329 Z= 0.150 Angle : 0.641 10.780 22268 Z= 0.317 Chirality : 0.046 0.364 2548 Planarity : 0.003 0.034 2706 Dihedral : 6.317 58.059 2847 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.87 % Allowed : 18.28 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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 (0.20), residues: 1889 helix: 2.31 (0.21), residues: 578 sheet: 0.72 (0.23), residues: 519 loop : 0.61 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 426 HIS 0.002 0.001 HIS A 143 PHE 0.018 0.001 PHE D 307 TYR 0.025 0.001 TYR B 299 ARG 0.003 0.000 ARG D 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 13) link_NAG-ASN : angle 1.76939 ( 39) link_ALPHA1-6 : bond 0.00900 ( 4) link_ALPHA1-6 : angle 1.61999 ( 12) link_BETA1-4 : bond 0.00450 ( 11) link_BETA1-4 : angle 1.53376 ( 33) link_ALPHA1-3 : bond 0.00921 ( 4) link_ALPHA1-3 : angle 1.74926 ( 12) hydrogen bonds : bond 0.03647 ( 816) hydrogen bonds : angle 4.33209 ( 2552) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.36440 ( 14) covalent geometry : bond 0.00343 (16290) covalent geometry : angle 0.63355 (22158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8914 (mp0) REVERT: A 92 GLU cc_start: 0.8956 (pt0) cc_final: 0.8403 (pm20) REVERT: A 131 ASP cc_start: 0.9225 (p0) cc_final: 0.8644 (p0) REVERT: A 155 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8221 (mpp) REVERT: A 319 MET cc_start: 0.9196 (ttp) cc_final: 0.8906 (ttm) REVERT: A 345 ASN cc_start: 0.8385 (m110) cc_final: 0.7953 (m110) REVERT: B 49 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8174 (pp-130) REVERT: B 223 LEU cc_start: 0.9486 (tp) cc_final: 0.9198 (pp) REVERT: B 224 GLN cc_start: 0.9009 (tp40) cc_final: 0.8748 (tp40) REVERT: B 244 TYR cc_start: 0.8619 (p90) cc_final: 0.8407 (p90) REVERT: B 425 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8046 (mpt180) REVERT: B 437 LEU cc_start: 0.8707 (tm) cc_final: 0.8319 (mp) REVERT: C 49 MET cc_start: 0.8388 (tmm) cc_final: 0.8002 (ppp) REVERT: C 190 GLU cc_start: 0.8929 (tt0) cc_final: 0.8552 (pt0) REVERT: C 255 ILE cc_start: 0.9420 (pp) cc_final: 0.9202 (pp) REVERT: C 274 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8921 (mmmm) REVERT: C 286 MET cc_start: 0.8142 (mmm) cc_final: 0.7568 (mtm) REVERT: C 301 PHE cc_start: 0.8781 (t80) cc_final: 0.8192 (t80) REVERT: D 9 MET cc_start: 0.8055 (mtp) cc_final: 0.7619 (mpp) REVERT: D 95 ASP cc_start: 0.9084 (p0) cc_final: 0.8648 (p0) REVERT: D 220 TYR cc_start: 0.8630 (t80) cc_final: 0.8385 (t80) REVERT: D 286 MET cc_start: 0.8911 (mtm) cc_final: 0.8572 (mtm) REVERT: D 426 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: E 83 MET cc_start: 0.9262 (mmm) cc_final: 0.9061 (tpp) REVERT: E 147 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: E 170 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8569 (mttm) REVERT: E 173 MET cc_start: 0.9355 (mtm) cc_final: 0.9084 (mpp) REVERT: E 179 MET cc_start: 0.8845 (mpp) cc_final: 0.8501 (mpp) REVERT: E 208 LYS cc_start: 0.9290 (mttp) cc_final: 0.9079 (mppt) REVERT: E 210 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: E 233 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8215 (tp40) REVERT: E 308 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8303 (mtmp) REVERT: F 458 SER cc_start: 0.9076 (t) cc_final: 0.8680 (p) REVERT: F 459 ARG cc_start: 0.8223 (pmt170) cc_final: 0.7955 (pmt170) REVERT: F 469 GLU cc_start: 0.8711 (mp0) cc_final: 0.8216 (mp0) REVERT: F 470 MET cc_start: 0.8862 (mtp) cc_final: 0.8440 (mtm) REVERT: F 473 LEU cc_start: 0.8780 (tt) cc_final: 0.8304 (mp) REVERT: F 501 TYR cc_start: 0.9072 (m-80) cc_final: 0.8830 (m-80) REVERT: G 1 GLN cc_start: 0.8322 (mp10) cc_final: 0.7977 (pm20) REVERT: G 433 GLU cc_start: 0.8456 (pp20) cc_final: 0.8143 (pp20) REVERT: G 440 TRP cc_start: 0.8490 (m100) cc_final: 0.8224 (m100) REVERT: G 469 GLU cc_start: 0.8184 (mp0) cc_final: 0.7547 (mp0) REVERT: G 470 MET cc_start: 0.8625 (mtm) cc_final: 0.8263 (mtp) REVERT: G 472 ASN cc_start: 0.9238 (m-40) cc_final: 0.8618 (t0) REVERT: G 474 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7624 (mptm) REVERT: G 504 GLN cc_start: 0.8467 (pm20) cc_final: 0.8244 (pm20) outliers start: 47 outliers final: 20 residues processed: 293 average time/residue: 1.1532 time to fit residues: 378.2898 Evaluate side-chains 289 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 0.0770 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 227 ASN E 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.058454 restraints weight = 131887.570| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 5.18 r_work: 0.2523 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16329 Z= 0.134 Angle : 0.653 11.468 22268 Z= 0.321 Chirality : 0.046 0.389 2548 Planarity : 0.003 0.033 2706 Dihedral : 6.067 54.793 2847 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.15 % Allowed : 19.35 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), residues: 1889 helix: 2.33 (0.21), residues: 578 sheet: 0.60 (0.22), residues: 541 loop : 0.70 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 PHE 0.020 0.001 PHE C 240 TYR 0.025 0.001 TYR E 318 ARG 0.003 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 13) link_NAG-ASN : angle 1.67046 ( 39) link_ALPHA1-6 : bond 0.00940 ( 4) link_ALPHA1-6 : angle 1.59902 ( 12) link_BETA1-4 : bond 0.00431 ( 11) link_BETA1-4 : angle 1.43316 ( 33) link_ALPHA1-3 : bond 0.00943 ( 4) link_ALPHA1-3 : angle 1.69117 ( 12) hydrogen bonds : bond 0.03555 ( 816) hydrogen bonds : angle 4.27258 ( 2552) SS BOND : bond 0.00116 ( 7) SS BOND : angle 0.31470 ( 14) covalent geometry : bond 0.00305 (16290) covalent geometry : angle 0.64649 (22158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8930 (mp0) REVERT: A 92 GLU cc_start: 0.8991 (pt0) cc_final: 0.8407 (pm20) REVERT: A 131 ASP cc_start: 0.9232 (p0) cc_final: 0.8617 (p0) REVERT: A 155 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8225 (mpp) REVERT: A 319 MET cc_start: 0.9181 (ttp) cc_final: 0.8900 (ttm) REVERT: A 345 ASN cc_start: 0.8406 (m110) cc_final: 0.7968 (m110) REVERT: B 49 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8148 (pp-130) REVERT: B 223 LEU cc_start: 0.9486 (tp) cc_final: 0.9197 (pp) REVERT: B 224 GLN cc_start: 0.8993 (tp40) cc_final: 0.8720 (tp40) REVERT: B 244 TYR cc_start: 0.8655 (p90) cc_final: 0.8454 (p90) REVERT: B 425 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8094 (mpt180) REVERT: B 437 LEU cc_start: 0.8666 (tm) cc_final: 0.8310 (mp) REVERT: C 49 MET cc_start: 0.8467 (tmm) cc_final: 0.8200 (pp-130) REVERT: C 190 GLU cc_start: 0.8972 (tt0) cc_final: 0.8587 (pt0) REVERT: C 255 ILE cc_start: 0.9408 (pp) cc_final: 0.9193 (pp) REVERT: C 274 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8911 (mmmm) REVERT: C 286 MET cc_start: 0.8163 (mmm) cc_final: 0.7657 (mtm) REVERT: C 301 PHE cc_start: 0.8790 (t80) cc_final: 0.8220 (t80) REVERT: D 9 MET cc_start: 0.8120 (mtp) cc_final: 0.7674 (mpp) REVERT: D 95 ASP cc_start: 0.9100 (p0) cc_final: 0.8682 (p0) REVERT: D 286 MET cc_start: 0.8935 (mtm) cc_final: 0.8592 (mtm) REVERT: D 426 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: E 83 MET cc_start: 0.9226 (mmm) cc_final: 0.9017 (tpp) REVERT: E 170 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8556 (mttm) REVERT: E 173 MET cc_start: 0.9349 (mtm) cc_final: 0.9077 (mpp) REVERT: E 179 MET cc_start: 0.8850 (mpp) cc_final: 0.8522 (mpp) REVERT: E 210 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: E 233 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8223 (tp40) REVERT: E 308 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8288 (mtmp) REVERT: F 458 SER cc_start: 0.9039 (t) cc_final: 0.8612 (p) REVERT: F 459 ARG cc_start: 0.8238 (pmt170) cc_final: 0.7991 (pmt170) REVERT: F 469 GLU cc_start: 0.8753 (mp0) cc_final: 0.8240 (mp0) REVERT: F 470 MET cc_start: 0.8857 (mtp) cc_final: 0.8456 (mtm) REVERT: F 473 LEU cc_start: 0.8793 (tt) cc_final: 0.8331 (mp) REVERT: F 501 TYR cc_start: 0.9074 (m-80) cc_final: 0.8853 (m-80) REVERT: G 1 GLN cc_start: 0.8378 (mp10) cc_final: 0.8036 (pm20) REVERT: G 433 GLU cc_start: 0.8478 (pp20) cc_final: 0.8202 (pp20) REVERT: G 440 TRP cc_start: 0.8385 (m100) cc_final: 0.8183 (m100) REVERT: G 459 ARG cc_start: 0.8445 (ppt90) cc_final: 0.8058 (ptt-90) REVERT: G 469 GLU cc_start: 0.8202 (mp0) cc_final: 0.7552 (mp0) REVERT: G 470 MET cc_start: 0.8670 (mtm) cc_final: 0.8219 (mtm) REVERT: G 472 ASN cc_start: 0.9231 (m-40) cc_final: 0.8742 (t0) REVERT: G 504 GLN cc_start: 0.8433 (pm20) cc_final: 0.8197 (pm20) outliers start: 35 outliers final: 21 residues processed: 289 average time/residue: 1.2175 time to fit residues: 395.3038 Evaluate side-chains 290 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 87 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 141 optimal weight: 0.0050 chunk 102 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN E 227 ASN E 253 GLN G 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.058305 restraints weight = 127112.735| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 5.09 r_work: 0.2519 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16329 Z= 0.147 Angle : 0.671 13.080 22268 Z= 0.330 Chirality : 0.046 0.402 2548 Planarity : 0.003 0.031 2706 Dihedral : 5.947 53.182 2847 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.15 % Allowed : 19.71 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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 (0.20), residues: 1889 helix: 2.30 (0.22), residues: 578 sheet: 0.52 (0.22), residues: 574 loop : 0.80 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 PHE 0.022 0.001 PHE C 240 TYR 0.025 0.001 TYR B 299 ARG 0.005 0.000 ARG G 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 13) link_NAG-ASN : angle 1.65387 ( 39) link_ALPHA1-6 : bond 0.00915 ( 4) link_ALPHA1-6 : angle 1.57983 ( 12) link_BETA1-4 : bond 0.00412 ( 11) link_BETA1-4 : angle 1.46511 ( 33) link_ALPHA1-3 : bond 0.00913 ( 4) link_ALPHA1-3 : angle 1.71472 ( 12) hydrogen bonds : bond 0.03608 ( 816) hydrogen bonds : angle 4.29028 ( 2552) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.34717 ( 14) covalent geometry : bond 0.00340 (16290) covalent geometry : angle 0.66461 (22158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8930 (mp0) REVERT: A 92 GLU cc_start: 0.8978 (pt0) cc_final: 0.8398 (pm20) REVERT: A 131 ASP cc_start: 0.9229 (p0) cc_final: 0.8624 (p0) REVERT: A 155 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8224 (mpp) REVERT: A 319 MET cc_start: 0.9182 (ttp) cc_final: 0.8952 (ttm) REVERT: B 49 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8165 (pp-130) REVERT: B 223 LEU cc_start: 0.9490 (tp) cc_final: 0.9195 (pp) REVERT: B 224 GLN cc_start: 0.9000 (tp40) cc_final: 0.8728 (tp40) REVERT: B 244 TYR cc_start: 0.8653 (p90) cc_final: 0.8452 (p90) REVERT: B 425 ARG cc_start: 0.8853 (ttt180) cc_final: 0.8089 (mpt180) REVERT: B 437 LEU cc_start: 0.8652 (tm) cc_final: 0.8302 (mp) REVERT: C 49 MET cc_start: 0.8504 (tmm) cc_final: 0.8237 (pp-130) REVERT: C 179 GLU cc_start: 0.8671 (pm20) cc_final: 0.8378 (pm20) REVERT: C 190 GLU cc_start: 0.8984 (tt0) cc_final: 0.8590 (pt0) REVERT: C 255 ILE cc_start: 0.9393 (pp) cc_final: 0.9181 (pp) REVERT: C 261 MET cc_start: 0.9283 (mmm) cc_final: 0.8996 (mmt) REVERT: C 274 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8932 (mmmm) REVERT: C 286 MET cc_start: 0.8162 (mmm) cc_final: 0.7647 (mtm) REVERT: C 301 PHE cc_start: 0.8786 (t80) cc_final: 0.8220 (t80) REVERT: D 9 MET cc_start: 0.8101 (mtp) cc_final: 0.7697 (mpp) REVERT: D 95 ASP cc_start: 0.9103 (p0) cc_final: 0.8681 (p0) REVERT: D 286 MET cc_start: 0.8957 (mtm) cc_final: 0.8605 (mtm) REVERT: D 426 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7899 (m-10) REVERT: E 147 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: E 170 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8576 (mttm) REVERT: E 179 MET cc_start: 0.8886 (mpp) cc_final: 0.8556 (mpp) REVERT: E 210 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: E 233 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8201 (tp40) REVERT: E 308 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8278 (mtmp) REVERT: F 458 SER cc_start: 0.9048 (t) cc_final: 0.8615 (p) REVERT: F 459 ARG cc_start: 0.8274 (pmt170) cc_final: 0.8040 (ppt90) REVERT: F 469 GLU cc_start: 0.8735 (mp0) cc_final: 0.8220 (mp0) REVERT: F 470 MET cc_start: 0.8878 (mtp) cc_final: 0.8484 (mtm) REVERT: F 473 LEU cc_start: 0.8794 (tt) cc_final: 0.8348 (mp) REVERT: F 501 TYR cc_start: 0.9073 (m-80) cc_final: 0.8829 (m-80) REVERT: G 1 GLN cc_start: 0.8346 (mp10) cc_final: 0.8034 (pm20) REVERT: G 433 GLU cc_start: 0.8484 (pp20) cc_final: 0.8200 (pp20) REVERT: G 469 GLU cc_start: 0.8155 (mp0) cc_final: 0.7443 (mp0) REVERT: G 470 MET cc_start: 0.8680 (mtm) cc_final: 0.8452 (mtp) REVERT: G 472 ASN cc_start: 0.9132 (m-40) cc_final: 0.8764 (t0) REVERT: G 504 GLN cc_start: 0.8440 (pm20) cc_final: 0.8210 (pm20) outliers start: 35 outliers final: 22 residues processed: 286 average time/residue: 1.1584 time to fit residues: 369.8102 Evaluate side-chains 292 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS 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 225 THR Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN E 227 ASN E 253 GLN G 414 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.056504 restraints weight = 128479.556| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 5.06 r_work: 0.2489 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16329 Z= 0.176 Angle : 0.685 13.096 22268 Z= 0.338 Chirality : 0.047 0.411 2548 Planarity : 0.003 0.032 2706 Dihedral : 5.988 53.274 2847 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.15 % Allowed : 20.07 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.61 (0.20), residues: 1889 helix: 2.26 (0.22), residues: 578 sheet: 0.62 (0.22), residues: 541 loop : 0.63 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 426 HIS 0.003 0.001 HIS E 240 PHE 0.018 0.001 PHE C 293 TYR 0.026 0.001 TYR B 299 ARG 0.003 0.000 ARG D 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 13) link_NAG-ASN : angle 1.71301 ( 39) link_ALPHA1-6 : bond 0.00893 ( 4) link_ALPHA1-6 : angle 1.60266 ( 12) link_BETA1-4 : bond 0.00437 ( 11) link_BETA1-4 : angle 1.54693 ( 33) link_ALPHA1-3 : bond 0.00861 ( 4) link_ALPHA1-3 : angle 1.72144 ( 12) hydrogen bonds : bond 0.03724 ( 816) hydrogen bonds : angle 4.34946 ( 2552) SS BOND : bond 0.00153 ( 7) SS BOND : angle 0.50518 ( 14) covalent geometry : bond 0.00409 (16290) covalent geometry : angle 0.67763 (22158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13549.81 seconds wall clock time: 233 minutes 0.76 seconds (13980.76 seconds total)