Starting phenix.real_space_refine on Thu Sep 18 10:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnc_14074/09_2025/7qnc_14074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnc_14074/09_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_14074/09_2025/7qnc_14074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnc_14074/09_2025/7qnc_14074.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnc_14074/09_2025/7qnc_14074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnc_14074/09_2025/7qnc_14074.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.62, per 1000 atoms: 0.35 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: 1.79 Conformation dependent library (CDL) restraints added in 926.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.73 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: 3.09 Time building geometry restraints manager: 2.22 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 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 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 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.790 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.002 ARG D 28 TYR 0.023 0.004 TYR B 157 PHE 0.019 0.001 PHE C 221 TRP 0.014 0.001 TRP G 440 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00310 (16290) covalent geometry : angle 0.58275 (22158) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.61942 ( 14) hydrogen bonds : bond 0.21645 ( 816) hydrogen bonds : angle 7.34191 ( 2552) link_ALPHA1-3 : bond 0.00040 ( 4) link_ALPHA1-3 : angle 0.46341 ( 12) 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_NAG-ASN : bond 0.03453 ( 13) link_NAG-ASN : angle 3.40303 ( 39) *********************** 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 : 0.630 Fit side-chains 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: 0.8089 (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: 0.8280 (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: 0.6450 time to fit residues: 303.0976 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 : 0.623 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.091016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.062891 restraints weight = 126870.763| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 5.21 r_work: 0.2637 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16329 Z= 0.144 Angle : 0.634 8.100 22268 Z= 0.325 Chirality : 0.044 0.188 2548 Planarity : 0.004 0.038 2706 Dihedral : 9.261 83.094 2847 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.46 % Allowed : 13.74 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.19), residues: 1889 helix: 2.25 (0.21), residues: 570 sheet: 1.08 (0.23), residues: 498 loop : 0.80 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 454 TYR 0.023 0.002 TYR C 299 PHE 0.023 0.002 PHE D 306 TRP 0.026 0.001 TRP C 426 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00307 (16290) covalent geometry : angle 0.62437 (22158) SS BOND : bond 0.00237 ( 7) SS BOND : angle 0.60494 ( 14) hydrogen bonds : bond 0.05760 ( 816) hydrogen bonds : angle 5.03838 ( 2552) link_ALPHA1-3 : bond 0.00897 ( 4) link_ALPHA1-3 : angle 2.15567 ( 12) link_ALPHA1-6 : bond 0.00652 ( 4) link_ALPHA1-6 : angle 1.54193 ( 12) link_BETA1-4 : bond 0.00452 ( 11) link_BETA1-4 : angle 1.52765 ( 33) link_NAG-ASN : bond 0.00234 ( 13) link_NAG-ASN : angle 1.91255 ( 39) *********************** 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 337 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8826 (mp0) REVERT: A 92 GLU cc_start: 0.8983 (pt0) cc_final: 0.8278 (pm20) REVERT: A 345 ASN cc_start: 0.8424 (m110) cc_final: 0.7903 (m110) REVERT: B 244 TYR cc_start: 0.8531 (p90) cc_final: 0.8090 (p90) REVERT: B 283 MET cc_start: 0.8836 (mmm) cc_final: 0.8608 (mmm) REVERT: B 425 ARG cc_start: 0.8851 (ttt180) cc_final: 0.8098 (mpt180) REVERT: C 55 MET cc_start: 0.9294 (mmm) cc_final: 0.9010 (mmt) REVERT: C 298 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 306 PHE cc_start: 0.8414 (t80) cc_final: 0.7872 (t80) REVERT: D 9 MET cc_start: 0.8069 (mtp) cc_final: 0.7406 (ttm) REVERT: D 49 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8100 (ptp) REVERT: D 95 ASP cc_start: 0.9005 (p0) cc_final: 0.8646 (p0) REVERT: D 220 TYR cc_start: 0.8582 (t80) cc_final: 0.8315 (t80) REVERT: D 223 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8709 (pp) REVERT: D 244 TYR cc_start: 0.8744 (p90) cc_final: 0.8517 (p90) REVERT: D 426 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.7992 (m-10) REVERT: E 142 LYS cc_start: 0.9391 (mttt) cc_final: 0.9170 (mttp) REVERT: E 179 MET cc_start: 0.8829 (mpp) cc_final: 0.8516 (mpp) REVERT: E 219 TYR cc_start: 0.9126 (p90) cc_final: 0.8820 (p90) REVERT: E 226 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6849 (tmt) REVERT: F 407 LEU cc_start: 0.9052 (mt) cc_final: 0.8701 (mm) REVERT: F 415 THR cc_start: 0.9165 (p) cc_final: 0.8791 (m) REVERT: F 426 GLN cc_start: 0.9013 (tt0) cc_final: 0.8316 (tp-100) REVERT: F 433 GLU cc_start: 0.8921 (pt0) cc_final: 0.8589 (pt0) REVERT: F 469 GLU cc_start: 0.8439 (mp0) cc_final: 0.8237 (mp0) REVERT: F 470 MET cc_start: 0.8675 (mtm) cc_final: 0.8274 (mtt) REVERT: F 481 TYR cc_start: 0.7672 (m-80) cc_final: 0.7262 (m-80) REVERT: G 467 TYR cc_start: 0.6810 (p90) cc_final: 0.6545 (OUTLIER) REVERT: G 469 GLU cc_start: 0.7495 (mp0) cc_final: 0.7153 (mp0) outliers start: 57 outliers final: 23 residues processed: 308 average time/residue: 0.5536 time to fit residues: 190.6702 Evaluate side-chains 275 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 HIS 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 301 PHE 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 49 MET Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 223 LEU 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 225 LEU Chi-restraints excluded: chain E residue 226 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 408 SER Chi-restraints excluded: chain G residue 441 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.059924 restraints weight = 132651.337| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 5.32 r_work: 0.2568 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16329 Z= 0.162 Angle : 0.624 8.822 22268 Z= 0.318 Chirality : 0.045 0.276 2548 Planarity : 0.004 0.040 2706 Dihedral : 8.328 72.485 2847 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.52 % Allowed : 14.52 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.20), residues: 1889 helix: 2.23 (0.21), residues: 582 sheet: 0.93 (0.23), residues: 515 loop : 0.81 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 454 TYR 0.028 0.002 TYR C 299 PHE 0.019 0.002 PHE D 221 TRP 0.029 0.002 TRP C 426 HIS 0.005 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00371 (16290) covalent geometry : angle 0.61497 (22158) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.46718 ( 14) hydrogen bonds : bond 0.04539 ( 816) hydrogen bonds : angle 4.61809 ( 2552) link_ALPHA1-3 : bond 0.00985 ( 4) link_ALPHA1-3 : angle 1.81396 ( 12) link_ALPHA1-6 : bond 0.00767 ( 4) link_ALPHA1-6 : angle 1.70238 ( 12) link_BETA1-4 : bond 0.00430 ( 11) link_BETA1-4 : angle 1.56887 ( 33) link_NAG-ASN : bond 0.00303 ( 13) link_NAG-ASN : angle 1.81759 ( 39) *********************** 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 337 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8861 (mp0) REVERT: A 92 GLU cc_start: 0.8970 (pt0) cc_final: 0.8275 (pm20) REVERT: A 131 ASP cc_start: 0.9150 (p0) cc_final: 0.8584 (p0) REVERT: A 155 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8408 (mpp) REVERT: A 345 ASN cc_start: 0.8422 (m110) cc_final: 0.7941 (m110) REVERT: B 49 MET cc_start: 0.8512 (tmm) cc_final: 0.8152 (pp-130) REVERT: B 52 GLU cc_start: 0.8769 (mp0) cc_final: 0.8563 (mp0) REVERT: B 190 GLU cc_start: 0.8935 (tt0) cc_final: 0.8704 (pt0) REVERT: B 223 LEU cc_start: 0.9486 (tp) cc_final: 0.9213 (tp) REVERT: B 244 TYR cc_start: 0.8554 (p90) cc_final: 0.8218 (p90) REVERT: B 425 ARG cc_start: 0.8879 (ttt180) cc_final: 0.8112 (mpt180) REVERT: B 440 LEU cc_start: 0.8839 (tp) cc_final: 0.8497 (tt) REVERT: C 55 MET cc_start: 0.9337 (mmm) cc_final: 0.9095 (mmm) REVERT: C 286 MET cc_start: 0.8249 (mmm) cc_final: 0.7741 (mtt) REVERT: C 301 PHE cc_start: 0.8935 (m-80) cc_final: 0.8728 (t80) REVERT: C 306 PHE cc_start: 0.8391 (t80) cc_final: 0.7695 (t80) REVERT: D 9 MET cc_start: 0.8148 (mtp) cc_final: 0.7554 (ttm) REVERT: D 95 ASP cc_start: 0.9086 (p0) cc_final: 0.8686 (p0) REVERT: D 181 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7754 (mm) REVERT: D 220 TYR cc_start: 0.8680 (t80) cc_final: 0.8340 (t80) REVERT: D 223 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8715 (pp) REVERT: D 244 TYR cc_start: 0.8600 (p90) cc_final: 0.8381 (p90) REVERT: D 426 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.8039 (m-10) REVERT: E 142 LYS cc_start: 0.9418 (mttt) cc_final: 0.9209 (mttp) REVERT: E 179 MET cc_start: 0.8834 (mpp) cc_final: 0.8501 (mpp) REVERT: E 210 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: E 273 GLN cc_start: 0.8025 (pm20) cc_final: 0.7812 (pm20) REVERT: F 407 LEU cc_start: 0.9132 (mt) cc_final: 0.8791 (mm) REVERT: F 415 THR cc_start: 0.9220 (p) cc_final: 0.8837 (m) REVERT: F 426 GLN cc_start: 0.9073 (tt0) cc_final: 0.8407 (tp-100) REVERT: F 433 GLU cc_start: 0.8951 (pt0) cc_final: 0.8651 (pt0) REVERT: F 472 ASN cc_start: 0.8435 (m-40) cc_final: 0.8216 (m-40) REVERT: F 481 TYR cc_start: 0.8074 (m-80) cc_final: 0.7767 (m-80) REVERT: G 1 GLN cc_start: 0.8417 (mp10) cc_final: 0.7710 (pm20) REVERT: G 414 HIS cc_start: 0.8789 (m90) cc_final: 0.8575 (m170) REVERT: G 454 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7324 (ttp80) REVERT: G 460 ASP cc_start: 0.6215 (p0) cc_final: 0.5948 (p0) REVERT: G 469 GLU cc_start: 0.7780 (mp0) cc_final: 0.7359 (mp0) REVERT: G 476 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8837 (tp30) REVERT: G 481 TYR cc_start: 0.7718 (m-80) cc_final: 0.7458 (m-10) REVERT: G 504 GLN cc_start: 0.8513 (pm20) cc_final: 0.8294 (pm20) outliers start: 57 outliers final: 15 residues processed: 309 average time/residue: 0.5797 time to fit residues: 199.2920 Evaluate side-chains 270 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 264 MET 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 7 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 177 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 162 optimal weight: 0.0040 chunk 81 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN A C 243 ASN C 265 ASN D 265 ASN E 77 HIS E 213 GLN E 227 ASN ** 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 = 0.3346 r_free = 0.3346 target = 0.086649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.057662 restraints weight = 122963.842| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 5.09 r_work: 0.2529 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 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 = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 16329 Z= 0.209 Angle : 0.649 10.017 22268 Z= 0.329 Chirality : 0.046 0.224 2548 Planarity : 0.004 0.038 2706 Dihedral : 7.903 69.770 2847 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.52 % Allowed : 15.23 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.20), residues: 1889 helix: 2.31 (0.21), residues: 576 sheet: 0.95 (0.23), residues: 515 loop : 0.68 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 459 TYR 0.031 0.002 TYR C 299 PHE 0.019 0.002 PHE D 221 TRP 0.031 0.002 TRP C 426 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00482 (16290) covalent geometry : angle 0.63852 (22158) SS BOND : bond 0.00223 ( 7) SS BOND : angle 0.56112 ( 14) hydrogen bonds : bond 0.04237 ( 816) hydrogen bonds : angle 4.55479 ( 2552) link_ALPHA1-3 : bond 0.00845 ( 4) link_ALPHA1-3 : angle 2.00357 ( 12) link_ALPHA1-6 : bond 0.00729 ( 4) link_ALPHA1-6 : angle 1.77270 ( 12) link_BETA1-4 : bond 0.00428 ( 11) link_BETA1-4 : angle 1.69040 ( 33) link_NAG-ASN : bond 0.00368 ( 13) link_NAG-ASN : angle 1.96975 ( 39) *********************** 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: 58 poor density : 267 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9028 (mp0) REVERT: A 92 GLU cc_start: 0.8951 (pt0) cc_final: 0.8421 (pm20) REVERT: A 131 ASP cc_start: 0.9189 (p0) cc_final: 0.8643 (p0) REVERT: A 155 MET cc_start: 0.9283 (mtm) cc_final: 0.8436 (mpp) REVERT: A 345 ASN cc_start: 0.8374 (m110) cc_final: 0.7924 (m110) REVERT: B 49 MET cc_start: 0.8567 (tmm) cc_final: 0.8170 (pp-130) REVERT: B 223 LEU cc_start: 0.9470 (tp) cc_final: 0.9149 (tp) REVERT: B 224 GLN cc_start: 0.9123 (tp40) cc_final: 0.8910 (tp40) REVERT: B 244 TYR cc_start: 0.8595 (p90) cc_final: 0.8301 (p90) REVERT: B 425 ARG cc_start: 0.8893 (ttt180) cc_final: 0.8106 (mpt180) REVERT: B 440 LEU cc_start: 0.8920 (tp) cc_final: 0.8568 (tt) REVERT: C 55 MET cc_start: 0.9384 (mmm) cc_final: 0.9101 (mmm) REVERT: C 255 ILE cc_start: 0.9443 (pp) cc_final: 0.9183 (pp) REVERT: C 274 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8915 (mmmm) REVERT: C 286 MET cc_start: 0.8307 (mmm) cc_final: 0.7834 (mtt) REVERT: C 301 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (t80) REVERT: C 306 PHE cc_start: 0.8349 (t80) cc_final: 0.7732 (t80) REVERT: D 9 MET cc_start: 0.8094 (mtp) cc_final: 0.7531 (ttm) REVERT: D 95 ASP cc_start: 0.9107 (p0) cc_final: 0.8679 (p0) REVERT: D 286 MET cc_start: 0.8947 (mtm) cc_final: 0.8583 (mtm) REVERT: D 426 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: E 142 LYS cc_start: 0.9423 (mttt) cc_final: 0.9214 (mttp) REVERT: E 170 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8569 (mttm) REVERT: E 173 MET cc_start: 0.9363 (mtm) cc_final: 0.9140 (mpp) REVERT: E 179 MET cc_start: 0.8899 (mpp) cc_final: 0.8568 (mpp) REVERT: E 210 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: F 407 LEU cc_start: 0.9271 (mt) cc_final: 0.8939 (mm) REVERT: F 426 GLN cc_start: 0.9104 (tt0) cc_final: 0.8875 (tt0) REVERT: F 458 SER cc_start: 0.8996 (t) cc_final: 0.8584 (p) REVERT: F 469 GLU cc_start: 0.8632 (mp0) cc_final: 0.8310 (mp0) REVERT: F 470 MET cc_start: 0.8637 (mtp) cc_final: 0.8265 (mtm) REVERT: F 472 ASN cc_start: 0.8725 (m-40) cc_final: 0.8499 (m-40) REVERT: G 407 LEU cc_start: 0.8774 (mp) cc_final: 0.8496 (mp) REVERT: G 433 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8275 (pp20) REVERT: G 440 TRP cc_start: 0.8741 (m100) cc_final: 0.8361 (m100) REVERT: G 469 GLU cc_start: 0.7940 (mp0) cc_final: 0.7610 (mp0) REVERT: G 470 MET cc_start: 0.8373 (mtt) cc_final: 0.7988 (mpp) REVERT: G 472 ASN cc_start: 0.8967 (m-40) cc_final: 0.8241 (t0) REVERT: G 474 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7480 (mttp) REVERT: G 476 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8788 (tp30) REVERT: G 504 GLN cc_start: 0.8522 (pm20) cc_final: 0.8290 (pm20) outliers start: 58 outliers final: 20 residues processed: 290 average time/residue: 0.5681 time to fit residues: 183.8725 Evaluate side-chains 280 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN 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 301 PHE Chi-restraints excluded: chain D residue 426 TRP 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 E residue 264 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 97 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 0.0060 chunk 165 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 43 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.057907 restraints weight = 120879.391| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 5.02 r_work: 0.2529 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16329 Z= 0.177 Angle : 0.624 10.012 22268 Z= 0.316 Chirality : 0.046 0.265 2548 Planarity : 0.004 0.039 2706 Dihedral : 7.481 66.937 2847 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.52 % Allowed : 16.31 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.20), residues: 1889 helix: 2.30 (0.21), residues: 579 sheet: 0.94 (0.23), residues: 515 loop : 0.60 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 454 TYR 0.029 0.002 TYR G 481 PHE 0.027 0.002 PHE D 221 TRP 0.031 0.002 TRP C 426 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00403 (16290) covalent geometry : angle 0.61534 (22158) SS BOND : bond 0.00165 ( 7) SS BOND : angle 0.43123 ( 14) hydrogen bonds : bond 0.04033 ( 816) hydrogen bonds : angle 4.43656 ( 2552) link_ALPHA1-3 : bond 0.00931 ( 4) link_ALPHA1-3 : angle 1.84962 ( 12) link_ALPHA1-6 : bond 0.00820 ( 4) link_ALPHA1-6 : angle 1.79758 ( 12) link_BETA1-4 : bond 0.00396 ( 11) link_BETA1-4 : angle 1.58382 ( 33) link_NAG-ASN : bond 0.00213 ( 13) link_NAG-ASN : angle 1.78157 ( 39) *********************** 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 323 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8999 (mp0) REVERT: A 92 GLU cc_start: 0.8973 (pt0) cc_final: 0.8443 (pm20) REVERT: A 131 ASP cc_start: 0.9217 (p0) cc_final: 0.8664 (p0) REVERT: A 155 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8399 (mpp) REVERT: A 319 MET cc_start: 0.9176 (ttp) cc_final: 0.8971 (ttm) REVERT: A 345 ASN cc_start: 0.8359 (m110) cc_final: 0.7921 (m110) REVERT: B 49 MET cc_start: 0.8630 (tmm) cc_final: 0.8245 (pp-130) REVERT: B 223 LEU cc_start: 0.9483 (tp) cc_final: 0.9135 (pp) REVERT: B 244 TYR cc_start: 0.8609 (p90) cc_final: 0.8314 (p90) REVERT: B 425 ARG cc_start: 0.8845 (ttt180) cc_final: 0.8044 (mpt180) REVERT: B 440 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8542 (tt) REVERT: C 49 MET cc_start: 0.8257 (tmm) cc_final: 0.8008 (pp-130) REVERT: C 55 MET cc_start: 0.9398 (mmm) cc_final: 0.9099 (mmm) REVERT: C 255 ILE cc_start: 0.9449 (pp) cc_final: 0.9199 (pp) REVERT: C 261 MET cc_start: 0.9305 (mmm) cc_final: 0.9075 (mmt) REVERT: C 274 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8921 (mmmm) REVERT: C 286 MET cc_start: 0.8265 (mmm) cc_final: 0.7714 (mtt) REVERT: C 301 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8717 (t80) REVERT: C 306 PHE cc_start: 0.8310 (t80) cc_final: 0.7553 (t80) REVERT: D 95 ASP cc_start: 0.9114 (p0) cc_final: 0.8693 (p0) REVERT: D 286 MET cc_start: 0.8922 (mtm) cc_final: 0.8681 (mtm) REVERT: D 426 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: E 142 LYS cc_start: 0.9405 (mttt) cc_final: 0.9201 (mttp) REVERT: E 170 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: E 179 MET cc_start: 0.8898 (mpp) cc_final: 0.8562 (mpp) REVERT: F 407 LEU cc_start: 0.9326 (mt) cc_final: 0.8971 (mm) REVERT: F 426 GLN cc_start: 0.9141 (tt0) cc_final: 0.8888 (tt0) REVERT: F 458 SER cc_start: 0.8968 (t) cc_final: 0.8570 (p) REVERT: F 469 GLU cc_start: 0.8742 (mp0) cc_final: 0.8330 (mp0) REVERT: F 470 MET cc_start: 0.8788 (mtp) cc_final: 0.8476 (mtm) REVERT: F 472 ASN cc_start: 0.8883 (m-40) cc_final: 0.8661 (m-40) REVERT: G 1 GLN cc_start: 0.8376 (mp10) cc_final: 0.7917 (pm20) REVERT: G 433 GLU cc_start: 0.8460 (pp20) cc_final: 0.8173 (pp20) REVERT: G 440 TRP cc_start: 0.8720 (m100) cc_final: 0.8424 (m100) REVERT: G 469 GLU cc_start: 0.7915 (mp0) cc_final: 0.7421 (mp0) REVERT: G 470 MET cc_start: 0.8445 (mtt) cc_final: 0.8209 (mtm) REVERT: G 472 ASN cc_start: 0.9040 (m-40) cc_final: 0.8385 (t0) REVERT: G 474 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7595 (mttp) REVERT: G 476 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8886 (tp30) outliers start: 58 outliers final: 23 residues processed: 290 average time/residue: 0.6005 time to fit residues: 194.0798 Evaluate side-chains 280 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 59 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 301 PHE 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 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 227 MET Chi-restraints excluded: chain D residue 283 MET 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 170 LYS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 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 181 optimal weight: 0.0970 chunk 99 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 243 ASN D 265 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 213 GLN E 227 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.059220 restraints weight = 122743.299| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 5.09 r_work: 0.2565 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16329 Z= 0.123 Angle : 0.629 9.863 22268 Z= 0.311 Chirality : 0.045 0.328 2548 Planarity : 0.003 0.038 2706 Dihedral : 6.795 61.109 2847 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.11 % Allowed : 17.20 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.20), residues: 1889 helix: 2.29 (0.21), residues: 582 sheet: 0.77 (0.22), residues: 543 loop : 0.73 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 114 TYR 0.037 0.001 TYR G 481 PHE 0.016 0.001 PHE C 293 TRP 0.032 0.001 TRP C 426 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00276 (16290) covalent geometry : angle 0.62071 (22158) SS BOND : bond 0.00121 ( 7) SS BOND : angle 0.39312 ( 14) hydrogen bonds : bond 0.03718 ( 816) hydrogen bonds : angle 4.30658 ( 2552) link_ALPHA1-3 : bond 0.01056 ( 4) link_ALPHA1-3 : angle 1.80161 ( 12) link_ALPHA1-6 : bond 0.00953 ( 4) link_ALPHA1-6 : angle 1.74434 ( 12) link_BETA1-4 : bond 0.00419 ( 11) link_BETA1-4 : angle 1.42050 ( 33) link_NAG-ASN : bond 0.00212 ( 13) link_NAG-ASN : angle 1.90376 ( 39) *********************** 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 324 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9040 (mp0) REVERT: A 92 GLU cc_start: 0.8974 (pt0) cc_final: 0.8425 (pm20) REVERT: A 131 ASP cc_start: 0.9210 (p0) cc_final: 0.8679 (p0) REVERT: A 155 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8346 (mpp) REVERT: A 319 MET cc_start: 0.9193 (ttp) cc_final: 0.8948 (ttm) REVERT: A 345 ASN cc_start: 0.8353 (m110) cc_final: 0.7926 (m110) REVERT: B 49 MET cc_start: 0.8702 (tmm) cc_final: 0.8300 (pp-130) REVERT: B 223 LEU cc_start: 0.9499 (tp) cc_final: 0.9159 (pp) REVERT: B 244 TYR cc_start: 0.8613 (p90) cc_final: 0.8326 (p90) REVERT: B 425 ARG cc_start: 0.8839 (ttt180) cc_final: 0.8037 (mpt180) REVERT: B 437 LEU cc_start: 0.8767 (tm) cc_final: 0.8337 (mp) REVERT: B 440 LEU cc_start: 0.8893 (tp) cc_final: 0.8551 (tt) REVERT: C 49 MET cc_start: 0.8300 (tmm) cc_final: 0.8045 (pp-130) REVERT: C 55 MET cc_start: 0.9382 (mmm) cc_final: 0.9154 (mmm) REVERT: C 190 GLU cc_start: 0.8860 (tt0) cc_final: 0.8505 (pt0) REVERT: C 255 ILE cc_start: 0.9442 (pp) cc_final: 0.9205 (pp) REVERT: C 274 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8922 (mmmm) REVERT: C 286 MET cc_start: 0.8252 (mmm) cc_final: 0.7703 (mtt) REVERT: C 301 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8570 (t80) REVERT: C 429 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8685 (mp) REVERT: D 95 ASP cc_start: 0.9102 (p0) cc_final: 0.8706 (p0) REVERT: D 286 MET cc_start: 0.8923 (mtm) cc_final: 0.8713 (mtm) REVERT: D 426 TRP cc_start: 0.8369 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: E 147 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: E 179 MET cc_start: 0.8828 (mpp) cc_final: 0.8533 (mpp) REVERT: E 226 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6779 (tmt) REVERT: E 288 LEU cc_start: 0.8816 (mt) cc_final: 0.8550 (pp) REVERT: F 2 VAL cc_start: 0.9326 (t) cc_final: 0.9091 (m) REVERT: F 458 SER cc_start: 0.8932 (t) cc_final: 0.8517 (p) REVERT: F 469 GLU cc_start: 0.8758 (mp0) cc_final: 0.8288 (mp0) REVERT: F 470 MET cc_start: 0.8837 (mtp) cc_final: 0.8383 (mtm) REVERT: F 472 ASN cc_start: 0.8858 (m-40) cc_final: 0.8603 (m-40) REVERT: F 501 TYR cc_start: 0.9187 (m-80) cc_final: 0.8975 (m-80) REVERT: G 440 TRP cc_start: 0.8601 (m100) cc_final: 0.8374 (m100) REVERT: G 469 GLU cc_start: 0.7859 (mp0) cc_final: 0.7450 (mp0) REVERT: G 471 ASN cc_start: 0.8716 (m-40) cc_final: 0.8417 (m-40) REVERT: G 472 ASN cc_start: 0.9071 (m-40) cc_final: 0.8469 (t0) REVERT: G 474 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7669 (mttp) REVERT: G 476 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8796 (tp30) REVERT: G 478 THR cc_start: 0.8770 (m) cc_final: 0.8535 (p) outliers start: 51 outliers final: 19 residues processed: 294 average time/residue: 0.5683 time to fit residues: 186.8023 Evaluate side-chains 287 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 181 MET 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 274 LYS Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 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 E residue 147 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 264 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS E 227 ASN E 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.057666 restraints weight = 131563.788| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 5.24 r_work: 0.2529 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16329 Z= 0.166 Angle : 0.643 10.774 22268 Z= 0.321 Chirality : 0.046 0.361 2548 Planarity : 0.003 0.036 2706 Dihedral : 6.458 59.172 2847 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.75 % Allowed : 18.04 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1889 helix: 2.34 (0.21), residues: 579 sheet: 0.81 (0.23), residues: 543 loop : 0.70 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 454 TYR 0.027 0.002 TYR B 299 PHE 0.016 0.001 PHE C 293 TRP 0.034 0.002 TRP C 426 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00381 (16290) covalent geometry : angle 0.63481 (22158) SS BOND : bond 0.00180 ( 7) SS BOND : angle 0.41308 ( 14) hydrogen bonds : bond 0.03824 ( 816) hydrogen bonds : angle 4.33597 ( 2552) link_ALPHA1-3 : bond 0.00890 ( 4) link_ALPHA1-3 : angle 1.84142 ( 12) link_ALPHA1-6 : bond 0.00921 ( 4) link_ALPHA1-6 : angle 1.65109 ( 12) link_BETA1-4 : bond 0.00448 ( 11) link_BETA1-4 : angle 1.55490 ( 33) link_NAG-ASN : bond 0.00216 ( 13) link_NAG-ASN : angle 1.82890 ( 39) *********************** 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 309 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8977 (mp0) REVERT: A 92 GLU cc_start: 0.8990 (pt0) cc_final: 0.8457 (pm20) REVERT: A 131 ASP cc_start: 0.9221 (p0) cc_final: 0.8678 (p0) REVERT: A 155 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8380 (mpp) REVERT: A 319 MET cc_start: 0.9224 (ttp) cc_final: 0.8994 (ttm) REVERT: A 345 ASN cc_start: 0.8337 (m110) cc_final: 0.7894 (m110) REVERT: B 49 MET cc_start: 0.8704 (tmm) cc_final: 0.8299 (pp-130) REVERT: B 223 LEU cc_start: 0.9483 (tp) cc_final: 0.9160 (pp) REVERT: B 244 TYR cc_start: 0.8607 (p90) cc_final: 0.8331 (p90) REVERT: B 286 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7852 (mpp) REVERT: B 425 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8029 (mpt180) REVERT: B 437 LEU cc_start: 0.8737 (tm) cc_final: 0.8313 (mp) REVERT: B 440 LEU cc_start: 0.8859 (tp) cc_final: 0.8539 (tt) REVERT: C 49 MET cc_start: 0.8401 (tmm) cc_final: 0.8147 (pp-130) REVERT: C 190 GLU cc_start: 0.8880 (tt0) cc_final: 0.8517 (pt0) REVERT: C 255 ILE cc_start: 0.9452 (pp) cc_final: 0.9232 (pp) REVERT: C 261 MET cc_start: 0.9350 (mmm) cc_final: 0.9113 (mmt) REVERT: C 286 MET cc_start: 0.8267 (mmm) cc_final: 0.7699 (mtm) REVERT: C 301 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8581 (t80) REVERT: D 95 ASP cc_start: 0.9132 (p0) cc_final: 0.8722 (p0) REVERT: D 286 MET cc_start: 0.8947 (mtm) cc_final: 0.8739 (mtm) REVERT: D 426 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: E 170 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: E 179 MET cc_start: 0.8931 (mpp) cc_final: 0.8628 (mpp) REVERT: E 228 PHE cc_start: 0.8451 (m-80) cc_final: 0.8085 (m-80) REVERT: E 288 LEU cc_start: 0.8810 (mt) cc_final: 0.8511 (pp) REVERT: F 458 SER cc_start: 0.8938 (t) cc_final: 0.8512 (p) REVERT: F 469 GLU cc_start: 0.8778 (mp0) cc_final: 0.8317 (mp0) REVERT: F 470 MET cc_start: 0.8817 (mtp) cc_final: 0.8565 (mtm) REVERT: F 472 ASN cc_start: 0.8911 (m-40) cc_final: 0.8649 (m-40) REVERT: F 501 TYR cc_start: 0.9195 (m-80) cc_final: 0.8980 (m-80) REVERT: G 1 GLN cc_start: 0.8370 (mp10) cc_final: 0.7970 (pm20) REVERT: G 440 TRP cc_start: 0.8606 (m100) cc_final: 0.8356 (m100) REVERT: G 464 ASN cc_start: 0.9184 (m-40) cc_final: 0.8956 (m-40) REVERT: G 469 GLU cc_start: 0.8059 (mp0) cc_final: 0.7735 (mp0) REVERT: G 470 MET cc_start: 0.8213 (mmm) cc_final: 0.7931 (mpp) REVERT: G 471 ASN cc_start: 0.8813 (m-40) cc_final: 0.8508 (m-40) REVERT: G 472 ASN cc_start: 0.9148 (m-40) cc_final: 0.8504 (t0) REVERT: G 474 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7717 (mttp) REVERT: G 476 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8779 (tp30) REVERT: G 478 THR cc_start: 0.8829 (m) cc_final: 0.8572 (p) outliers start: 45 outliers final: 20 residues processed: 284 average time/residue: 0.5328 time to fit residues: 168.6322 Evaluate side-chains 285 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 59 LEU 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 301 PHE 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 E residue 170 LYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 441 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 243 ASN E 77 HIS E 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.058822 restraints weight = 136205.242| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 5.24 r_work: 0.2565 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16329 Z= 0.136 Angle : 0.651 10.984 22268 Z= 0.320 Chirality : 0.046 0.385 2548 Planarity : 0.003 0.036 2706 Dihedral : 6.151 55.682 2847 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.39 % Allowed : 18.76 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.20), residues: 1889 helix: 2.32 (0.21), residues: 579 sheet: 0.82 (0.23), residues: 543 loop : 0.72 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 432 TYR 0.025 0.001 TYR B 299 PHE 0.035 0.001 PHE D 306 TRP 0.035 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00310 (16290) covalent geometry : angle 0.64357 (22158) SS BOND : bond 0.00121 ( 7) SS BOND : angle 0.27939 ( 14) hydrogen bonds : bond 0.03679 ( 816) hydrogen bonds : angle 4.24190 ( 2552) link_ALPHA1-3 : bond 0.00936 ( 4) link_ALPHA1-3 : angle 1.67426 ( 12) link_ALPHA1-6 : bond 0.00951 ( 4) link_ALPHA1-6 : angle 1.62323 ( 12) link_BETA1-4 : bond 0.00431 ( 11) link_BETA1-4 : angle 1.42708 ( 33) link_NAG-ASN : bond 0.00160 ( 13) link_NAG-ASN : angle 1.77063 ( 39) *********************** 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 325 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8988 (mp0) REVERT: A 92 GLU cc_start: 0.8946 (pt0) cc_final: 0.8478 (pm20) REVERT: A 131 ASP cc_start: 0.9185 (p0) cc_final: 0.8642 (p0) REVERT: A 155 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8416 (mpp) REVERT: A 319 MET cc_start: 0.9233 (ttp) cc_final: 0.9022 (ttm) REVERT: A 345 ASN cc_start: 0.8344 (m110) cc_final: 0.7890 (m110) REVERT: B 49 MET cc_start: 0.8703 (tmm) cc_final: 0.8269 (pp-130) REVERT: B 223 LEU cc_start: 0.9494 (tp) cc_final: 0.9192 (pp) REVERT: B 244 TYR cc_start: 0.8591 (p90) cc_final: 0.8322 (p90) REVERT: B 286 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: B 425 ARG cc_start: 0.8808 (ttt180) cc_final: 0.8049 (mpt180) REVERT: B 437 LEU cc_start: 0.8802 (tm) cc_final: 0.8382 (mp) REVERT: B 440 LEU cc_start: 0.8874 (tp) cc_final: 0.8563 (tt) REVERT: C 49 MET cc_start: 0.8482 (tmm) cc_final: 0.8226 (pp-130) REVERT: C 55 MET cc_start: 0.9394 (mmm) cc_final: 0.9192 (mmm) REVERT: C 190 GLU cc_start: 0.8873 (tt0) cc_final: 0.8516 (pt0) REVERT: C 255 ILE cc_start: 0.9488 (pp) cc_final: 0.9265 (pp) REVERT: C 286 MET cc_start: 0.8256 (mmm) cc_final: 0.7722 (mtm) REVERT: C 301 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8585 (t80) REVERT: C 429 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8729 (mp) REVERT: D 95 ASP cc_start: 0.9093 (p0) cc_final: 0.8710 (p0) REVERT: D 233 THR cc_start: 0.9005 (m) cc_final: 0.8686 (p) REVERT: D 286 MET cc_start: 0.8971 (mtm) cc_final: 0.8766 (mtm) REVERT: D 426 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.7859 (m-10) REVERT: E 147 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: E 179 MET cc_start: 0.8851 (mpp) cc_final: 0.8588 (mpp) REVERT: E 210 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: E 233 GLN cc_start: 0.8788 (mt0) cc_final: 0.8358 (tp40) REVERT: F 414 HIS cc_start: 0.8829 (m90) cc_final: 0.8611 (m170) REVERT: F 458 SER cc_start: 0.8923 (t) cc_final: 0.8488 (p) REVERT: F 469 GLU cc_start: 0.8833 (mp0) cc_final: 0.8371 (mp0) REVERT: F 470 MET cc_start: 0.8875 (mtp) cc_final: 0.8628 (mtm) REVERT: F 473 LEU cc_start: 0.8777 (tt) cc_final: 0.8243 (mp) REVERT: G 1 GLN cc_start: 0.8319 (mp10) cc_final: 0.7778 (pm20) REVERT: G 440 TRP cc_start: 0.8430 (m100) cc_final: 0.8223 (m100) REVERT: G 464 ASN cc_start: 0.9218 (m-40) cc_final: 0.8994 (m-40) REVERT: G 469 GLU cc_start: 0.8112 (mp0) cc_final: 0.7576 (mp0) REVERT: G 471 ASN cc_start: 0.8882 (m-40) cc_final: 0.8653 (m-40) REVERT: G 472 ASN cc_start: 0.9159 (m-40) cc_final: 0.8638 (t0) REVERT: G 473 LEU cc_start: 0.9199 (mm) cc_final: 0.8962 (mp) REVERT: G 474 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7770 (mttp) REVERT: G 476 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8846 (tp30) REVERT: G 478 THR cc_start: 0.8905 (m) cc_final: 0.8671 (p) REVERT: G 480 VAL cc_start: 0.9006 (t) cc_final: 0.8784 (p) outliers start: 39 outliers final: 21 residues processed: 304 average time/residue: 0.5286 time to fit residues: 179.8290 Evaluate side-chains 304 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 535 MET 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 C residue 115 MET Chi-restraints excluded: chain C residue 301 PHE 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 E residue 89 VAL Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 264 MET 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 441 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 91 optimal weight: 0.9990 chunk 164 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS 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 = 0.3323 r_free = 0.3323 target = 0.085802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.057603 restraints weight = 132441.778| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 5.16 r_work: 0.2512 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16329 Z= 0.187 Angle : 0.685 11.645 22268 Z= 0.338 Chirality : 0.047 0.408 2548 Planarity : 0.003 0.033 2706 Dihedral : 6.229 56.210 2847 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.57 % Allowed : 19.53 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.20), residues: 1889 helix: 2.35 (0.22), residues: 578 sheet: 0.76 (0.23), residues: 543 loop : 0.63 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 269 TYR 0.027 0.002 TYR B 299 PHE 0.032 0.002 PHE D 306 TRP 0.037 0.002 TRP C 426 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00430 (16290) covalent geometry : angle 0.67739 (22158) SS BOND : bond 0.00155 ( 7) SS BOND : angle 0.47061 ( 14) hydrogen bonds : bond 0.03812 ( 816) hydrogen bonds : angle 4.33709 ( 2552) link_ALPHA1-3 : bond 0.00783 ( 4) link_ALPHA1-3 : angle 1.74235 ( 12) link_ALPHA1-6 : bond 0.00847 ( 4) link_ALPHA1-6 : angle 1.64130 ( 12) link_BETA1-4 : bond 0.00476 ( 11) link_BETA1-4 : angle 1.60201 ( 33) link_NAG-ASN : bond 0.00253 ( 13) link_NAG-ASN : angle 1.78170 ( 39) *********************** 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 314 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: A 92 GLU cc_start: 0.8977 (pt0) cc_final: 0.8414 (pm20) REVERT: A 131 ASP cc_start: 0.9245 (p0) cc_final: 0.8642 (p0) REVERT: A 155 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8337 (mpp) REVERT: A 319 MET cc_start: 0.9179 (ttp) cc_final: 0.8914 (ttm) REVERT: A 345 ASN cc_start: 0.8400 (m110) cc_final: 0.7967 (m110) REVERT: B 49 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8185 (pp-130) REVERT: B 223 LEU cc_start: 0.9474 (tp) cc_final: 0.9125 (pp) REVERT: B 244 TYR cc_start: 0.8626 (p90) cc_final: 0.8349 (p90) REVERT: B 286 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7829 (mpp) REVERT: B 425 ARG cc_start: 0.8867 (ttt180) cc_final: 0.8043 (mpt180) REVERT: B 437 LEU cc_start: 0.8728 (tm) cc_final: 0.8311 (mp) REVERT: B 440 LEU cc_start: 0.8838 (tp) cc_final: 0.8535 (tt) REVERT: C 49 MET cc_start: 0.8504 (tmm) cc_final: 0.8198 (pp-130) REVERT: C 190 GLU cc_start: 0.8956 (tt0) cc_final: 0.8567 (pt0) REVERT: C 255 ILE cc_start: 0.9414 (pp) cc_final: 0.9197 (pp) REVERT: C 286 MET cc_start: 0.8128 (mmm) cc_final: 0.7607 (mtm) REVERT: C 301 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8606 (t80) REVERT: D 95 ASP cc_start: 0.9094 (p0) cc_final: 0.8675 (p0) REVERT: D 147 GLU cc_start: 0.8819 (tt0) cc_final: 0.8531 (tm-30) REVERT: D 286 MET cc_start: 0.8931 (mtm) cc_final: 0.8702 (mtm) REVERT: D 426 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.7890 (m-10) REVERT: E 147 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: E 170 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8626 (mttm) REVERT: E 179 MET cc_start: 0.8916 (mpp) cc_final: 0.8583 (mpp) REVERT: E 208 LYS cc_start: 0.9261 (mttp) cc_final: 0.9038 (mppt) REVERT: E 210 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: E 308 LYS cc_start: 0.8706 (mtmp) cc_final: 0.8447 (mtmm) REVERT: F 1 GLN cc_start: 0.8577 (mp10) cc_final: 0.8285 (pm20) REVERT: F 458 SER cc_start: 0.9004 (t) cc_final: 0.8524 (p) REVERT: F 469 GLU cc_start: 0.8814 (mp0) cc_final: 0.8328 (mp0) REVERT: F 470 MET cc_start: 0.8924 (mtp) cc_final: 0.8657 (mtm) REVERT: F 473 LEU cc_start: 0.8808 (tt) cc_final: 0.8290 (mp) REVERT: G 1 GLN cc_start: 0.8344 (mp10) cc_final: 0.7904 (pm20) REVERT: G 469 GLU cc_start: 0.7988 (mp0) cc_final: 0.7421 (mp0) REVERT: G 471 ASN cc_start: 0.8926 (m-40) cc_final: 0.8712 (m-40) REVERT: G 472 ASN cc_start: 0.9228 (m-40) cc_final: 0.8625 (t0) REVERT: G 474 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7766 (mttp) REVERT: G 476 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8864 (tp30) REVERT: G 478 THR cc_start: 0.8975 (m) cc_final: 0.8739 (p) outliers start: 42 outliers final: 22 residues processed: 291 average time/residue: 0.5123 time to fit residues: 166.5212 Evaluate side-chains 290 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 49 MET 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 C residue 115 MET Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 PHE 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 59 LEU 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 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 264 MET 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 6 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 137 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 243 ASN E 227 ASN 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 = 0.086473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.058612 restraints weight = 129632.902| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 5.08 r_work: 0.2517 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16329 Z= 0.159 Angle : 0.686 12.066 22268 Z= 0.337 Chirality : 0.046 0.413 2548 Planarity : 0.003 0.034 2706 Dihedral : 6.056 54.203 2847 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.03 % Allowed : 20.67 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.20), residues: 1889 helix: 2.31 (0.22), residues: 578 sheet: 0.76 (0.23), residues: 543 loop : 0.62 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.026 0.001 TYR B 299 PHE 0.020 0.001 PHE C 240 TRP 0.037 0.002 TRP C 426 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00368 (16290) covalent geometry : angle 0.67956 (22158) SS BOND : bond 0.00124 ( 7) SS BOND : angle 0.40258 ( 14) hydrogen bonds : bond 0.03702 ( 816) hydrogen bonds : angle 4.28376 ( 2552) link_ALPHA1-3 : bond 0.00887 ( 4) link_ALPHA1-3 : angle 1.65523 ( 12) link_ALPHA1-6 : bond 0.00897 ( 4) link_ALPHA1-6 : angle 1.59503 ( 12) link_BETA1-4 : bond 0.00415 ( 11) link_BETA1-4 : angle 1.49794 ( 33) link_NAG-ASN : bond 0.00186 ( 13) link_NAG-ASN : angle 1.73067 ( 39) ********************** 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 305 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8906 (mp0) REVERT: A 92 GLU cc_start: 0.8989 (pt0) cc_final: 0.8390 (pm20) REVERT: A 131 ASP cc_start: 0.9252 (p0) cc_final: 0.8642 (p0) REVERT: A 155 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8306 (mpp) REVERT: A 319 MET cc_start: 0.9181 (ttp) cc_final: 0.8908 (ttm) REVERT: A 345 ASN cc_start: 0.8421 (m110) cc_final: 0.7980 (m110) REVERT: B 49 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8192 (pp-130) REVERT: B 223 LEU cc_start: 0.9474 (tp) cc_final: 0.9127 (pp) REVERT: B 244 TYR cc_start: 0.8627 (p90) cc_final: 0.8382 (p90) REVERT: B 286 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7854 (mpp) REVERT: B 425 ARG cc_start: 0.8847 (ttt180) cc_final: 0.8030 (mpt180) REVERT: B 437 LEU cc_start: 0.8717 (tm) cc_final: 0.8305 (mp) REVERT: B 440 LEU cc_start: 0.8837 (tp) cc_final: 0.8529 (tt) REVERT: C 49 MET cc_start: 0.8474 (tmm) cc_final: 0.8168 (pp-130) REVERT: C 190 GLU cc_start: 0.8961 (tt0) cc_final: 0.8521 (pt0) REVERT: C 255 ILE cc_start: 0.9399 (pp) cc_final: 0.9179 (pp) REVERT: C 286 MET cc_start: 0.8112 (mmm) cc_final: 0.7590 (mtm) REVERT: C 301 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8613 (t80) REVERT: D 95 ASP cc_start: 0.9089 (p0) cc_final: 0.8668 (p0) REVERT: D 233 THR cc_start: 0.8841 (m) cc_final: 0.8494 (p) REVERT: D 244 TYR cc_start: 0.8442 (p90) cc_final: 0.8157 (p90) REVERT: D 286 MET cc_start: 0.8943 (mtm) cc_final: 0.8706 (mtm) REVERT: D 426 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: E 147 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: E 179 MET cc_start: 0.8897 (mpp) cc_final: 0.8563 (mpp) REVERT: E 208 LYS cc_start: 0.9304 (mttp) cc_final: 0.9100 (mppt) REVERT: E 210 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: E 233 GLN cc_start: 0.8691 (mt0) cc_final: 0.8257 (tp40) REVERT: E 308 LYS cc_start: 0.8686 (mtmp) cc_final: 0.8410 (mtmm) REVERT: F 1 GLN cc_start: 0.8564 (mp10) cc_final: 0.8098 (pm20) REVERT: F 414 HIS cc_start: 0.8860 (m90) cc_final: 0.8604 (m170) REVERT: F 458 SER cc_start: 0.8984 (t) cc_final: 0.8515 (p) REVERT: F 467 TYR cc_start: 0.8596 (m-80) cc_final: 0.8383 (m-80) REVERT: F 469 GLU cc_start: 0.8836 (mp0) cc_final: 0.8286 (mp0) REVERT: F 470 MET cc_start: 0.8906 (mtp) cc_final: 0.8522 (mtm) REVERT: F 473 LEU cc_start: 0.8815 (tt) cc_final: 0.8316 (mp) REVERT: G 1 GLN cc_start: 0.8252 (mp10) cc_final: 0.7992 (pm20) REVERT: G 469 GLU cc_start: 0.7988 (mp0) cc_final: 0.7444 (mp0) REVERT: G 472 ASN cc_start: 0.9219 (m-40) cc_final: 0.8646 (t0) REVERT: G 474 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7709 (mttp) REVERT: G 478 THR cc_start: 0.8770 (m) cc_final: 0.8358 (p) outliers start: 33 outliers final: 20 residues processed: 289 average time/residue: 0.5224 time to fit residues: 169.2569 Evaluate side-chains 292 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 49 MET 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 C residue 115 MET Chi-restraints excluded: chain C residue 301 PHE 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 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 E residue 89 VAL Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 264 MET 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 102 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 104 optimal weight: 0.0770 chunk 89 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 overall best weight: 2.7344 ------------------------------------------------------------------------------- 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 G 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.055202 restraints weight = 117134.469| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 4.87 r_work: 0.2469 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16329 Z= 0.246 Angle : 0.740 12.344 22268 Z= 0.365 Chirality : 0.048 0.418 2548 Planarity : 0.004 0.032 2706 Dihedral : 6.390 57.647 2847 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.91 % Allowed : 20.73 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.20), residues: 1889 helix: 2.28 (0.22), residues: 575 sheet: 0.63 (0.23), residues: 547 loop : 0.62 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 459 TYR 0.030 0.002 TYR B 299 PHE 0.019 0.002 PHE C 293 TRP 0.037 0.002 TRP C 426 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00568 (16290) covalent geometry : angle 0.73144 (22158) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.63641 ( 14) hydrogen bonds : bond 0.04037 ( 816) hydrogen bonds : angle 4.43680 ( 2552) link_ALPHA1-3 : bond 0.00742 ( 4) link_ALPHA1-3 : angle 1.79523 ( 12) link_ALPHA1-6 : bond 0.00784 ( 4) link_ALPHA1-6 : angle 1.66536 ( 12) link_BETA1-4 : bond 0.00478 ( 11) link_BETA1-4 : angle 1.75633 ( 33) link_NAG-ASN : bond 0.00298 ( 13) link_NAG-ASN : angle 1.95660 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6448.12 seconds wall clock time: 110 minutes 30.32 seconds (6630.32 seconds total)