Starting phenix.real_space_refine on Sat May 17 21:42:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnc_14074/05_2025/7qnc_14074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnc_14074/05_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_14074/05_2025/7qnc_14074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnc_14074/05_2025/7qnc_14074.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnc_14074/05_2025/7qnc_14074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnc_14074/05_2025/7qnc_14074.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10316 2.51 5 N 2538 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15861 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2711 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 318} Chain breaks: 1 Chain: "B" Number of atoms: 2732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2703 Chain: "C" Number of atoms: 2767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2665 Chain: "D" Number of atoms: 2709 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2730 Chain: "E" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Chain: "F" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'D10': 1, 'EI7': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'D10': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'D10': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'EI7': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ATYR B 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 66 " occ=0.50 residue: pdb=" N AMET C 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET C 40 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N AILE C 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE C 164 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ALEU C 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 214 " occ=0.50 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 residue: pdb=" N HSM C 503 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 503 " occ=0.70 residue: pdb=" N HSM D 503 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 503 " occ=0.70 Time building chain proxies: 13.09, per 1000 atoms: 0.83 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: 4.41 Conformation dependent library (CDL) restraints added in 3.0 seconds 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 37.6% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 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: 6.27 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4797 1.34 - 1.46: 4329 1.46 - 1.58: 7003 1.58 - 1.69: 0 1.69 - 1.81: 161 Bond restraints: 16290 Sorted by residual: bond pdb=" N EI7 E 502 " pdb=" C EI7 E 502 " ideal model delta sigma weight residual 1.388 1.458 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N EI7 B 503 " pdb=" C EI7 B 503 " ideal model delta sigma weight residual 1.388 1.457 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C EI7 E 502 " pdb=" C2 EI7 E 502 " ideal model delta sigma weight residual 1.446 1.478 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C EI7 B 503 " pdb=" C2 EI7 B 503 " ideal model delta sigma weight residual 1.446 1.476 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 16285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 21573 1.60 - 3.19: 476 3.19 - 4.79: 80 4.79 - 6.39: 26 6.39 - 7.99: 3 Bond angle restraints: 22158 Sorted by residual: angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 113.86 7.99 1.19e+00 7.06e-01 4.50e+01 angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 113.89 7.96 1.19e+00 7.06e-01 4.48e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 113.94 7.91 1.19e+00 7.06e-01 4.42e+01 angle pdb=" N ILE B 305 " pdb=" CA ILE B 305 " pdb=" C ILE B 305 " ideal model delta sigma weight residual 113.42 107.89 5.53 1.17e+00 7.31e-01 2.24e+01 angle pdb=" N ILE C 305 " pdb=" CA ILE C 305 " pdb=" C ILE C 305 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9590 21.78 - 43.56: 292 43.56 - 65.34: 34 65.34 - 87.11: 34 87.11 - 108.89: 19 Dihedral angle restraints: 9969 sinusoidal: 4362 harmonic: 5607 Sorted by residual: dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2334 0.084 - 0.167: 199 0.167 - 0.251: 8 0.251 - 0.335: 5 0.335 - 0.418: 2 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.39e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.28e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.25e+01 ... (remaining 2545 not shown) Planarity restraints: 2719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 8 " 0.035 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN B 8 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 8 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 8 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " -0.037 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" CG ASN B 149 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.057 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 8 " 0.029 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" CG ASN C 8 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 8 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 8 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG C 502 " 0.037 2.00e-02 2.50e+03 ... (remaining 2716 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3941 2.80 - 3.33: 14468 3.33 - 3.85: 27253 3.85 - 4.38: 33104 4.38 - 4.90: 55430 Nonbonded interactions: 134196 Sorted by model distance: nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.276 3.120 nonbonded pdb=" NE ARG A 118 " pdb=" OD2 ASP B 163 " model vdw 2.283 3.120 nonbonded pdb=" O PHE E 439 " pdb=" ND2 ASN E 443 " model vdw 2.288 3.120 nonbonded pdb=" O ALA E 52 " pdb=" NH1 ARG E 99 " model vdw 2.326 3.120 nonbonded pdb=" OG SER A 232 " pdb=" OG1 THR A 247 " model vdw 2.328 3.040 ... (remaining 134191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) selection = (chain 'C' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) selection = (chain 'D' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.450 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16329 Z= 0.155 Angle : 0.601 9.017 22268 Z= 0.309 Chirality : 0.046 0.418 2548 Planarity : 0.005 0.057 2706 Dihedral : 12.798 108.892 6368 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.48 % Allowed : 3.29 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1889 helix: 0.80 (0.20), residues: 570 sheet: 0.99 (0.23), residues: 501 loop : 0.40 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 440 HIS 0.002 0.001 HIS E 92 PHE 0.019 0.001 PHE C 221 TYR 0.023 0.004 TYR B 157 ARG 0.014 0.002 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.03453 ( 13) link_NAG-ASN : angle 3.40303 ( 39) link_ALPHA1-6 : bond 0.00079 ( 4) link_ALPHA1-6 : angle 0.47613 ( 12) link_BETA1-4 : bond 0.00184 ( 11) link_BETA1-4 : angle 1.15365 ( 33) link_ALPHA1-3 : bond 0.00040 ( 4) link_ALPHA1-3 : angle 0.46341 ( 12) hydrogen bonds : bond 0.21645 ( 816) hydrogen bonds : angle 7.34191 ( 2552) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.61942 ( 14) covalent geometry : bond 0.00310 (16290) covalent geometry : angle 0.58275 (22158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 423 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8105 (pt0) cc_final: 0.7848 (pm20) REVERT: A 345 ASN cc_start: 0.8597 (m110) cc_final: 0.8186 (m110) REVERT: B 244 TYR cc_start: 0.8256 (p90) cc_final: 0.7693 (p90) REVERT: B 265 ASN cc_start: 0.8836 (t0) cc_final: 0.8596 (t0) REVERT: B 283 MET cc_start: 0.8669 (mmm) cc_final: 0.8409 (mmm) REVERT: B 425 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8039 (mpt180) REVERT: C 306 PHE cc_start: 0.8020 (t80) cc_final: 0.7102 (t80) REVERT: D 9 MET cc_start: 0.8261 (mtp) cc_final: 0.7816 (ttm) REVERT: E 142 LYS cc_start: 0.9019 (mttt) cc_final: 0.8775 (mttp) REVERT: E 170 LYS cc_start: 0.8774 (mttt) cc_final: 0.8518 (mtpm) REVERT: E 219 TYR cc_start: 0.8699 (p90) cc_final: 0.8373 (p90) REVERT: E 308 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8654 (mtmm) REVERT: F 407 LEU cc_start: 0.8932 (mt) cc_final: 0.8666 (mm) REVERT: F 415 THR cc_start: 0.9051 (p) cc_final: 0.8687 (m) REVERT: F 426 GLN cc_start: 0.8536 (tt0) cc_final: 0.8075 (tp-100) REVERT: F 465 THR cc_start: 0.8817 (m) cc_final: 0.8022 (m) REVERT: F 470 MET cc_start: 0.8282 (mtm) cc_final: 0.7943 (mtp) REVERT: F 481 TYR cc_start: 0.7497 (m-80) cc_final: 0.7173 (m-80) REVERT: G 412 SER cc_start: 0.9108 (p) cc_final: 0.8501 (p) REVERT: G 456 THR cc_start: 0.7957 (p) cc_final: 0.7645 (m) REVERT: G 457 ILE cc_start: 0.9018 (mt) cc_final: 0.8746 (mt) REVERT: G 458 SER cc_start: 0.8591 (t) cc_final: 0.8279 (t) REVERT: G 466 VAL cc_start: 0.8688 (t) cc_final: 0.8414 (m) REVERT: G 490 SER cc_start: 0.8873 (m) cc_final: 0.8573 (m) outliers start: 7 outliers final: 2 residues processed: 427 average time/residue: 1.2491 time to fit residues: 588.5636 Evaluate side-chains 248 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.0050 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 41 ASN B B 148 GLN C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 43 ASN E 77 HIS E 200 GLN E 227 ASN E 233 GLN E 253 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.058890 restraints weight = 115990.129| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 5.08 r_work: 0.2556 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16329 Z= 0.211 Angle : 0.681 8.727 22268 Z= 0.348 Chirality : 0.046 0.260 2548 Planarity : 0.004 0.039 2706 Dihedral : 9.151 80.684 2847 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.64 % Allowed : 13.38 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1889 helix: 2.22 (0.21), residues: 570 sheet: 1.01 (0.23), residues: 499 loop : 0.69 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 426 HIS 0.009 0.001 HIS B 267 PHE 0.024 0.002 PHE D 221 TYR 0.026 0.002 TYR C 299 ARG 0.009 0.001 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.01047 ( 13) link_NAG-ASN : angle 2.21858 ( 39) link_ALPHA1-6 : bond 0.00607 ( 4) link_ALPHA1-6 : angle 1.61756 ( 12) link_BETA1-4 : bond 0.00491 ( 11) link_BETA1-4 : angle 1.77786 ( 33) link_ALPHA1-3 : bond 0.00783 ( 4) link_ALPHA1-3 : angle 2.27272 ( 12) hydrogen bonds : bond 0.05486 ( 816) hydrogen bonds : angle 5.02880 ( 2552) SS BOND : bond 0.00283 ( 7) SS BOND : angle 0.75473 ( 14) covalent geometry : bond 0.00480 (16290) covalent geometry : angle 0.66914 (22158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: A 92 GLU cc_start: 0.9028 (pt0) cc_final: 0.8343 (pm20) REVERT: A 345 ASN cc_start: 0.8408 (m110) cc_final: 0.7908 (m110) REVERT: B 244 TYR cc_start: 0.8607 (p90) cc_final: 0.8228 (p90) REVERT: B 283 MET cc_start: 0.8869 (mmm) cc_final: 0.8636 (mmm) REVERT: B 425 ARG cc_start: 0.8897 (ttt180) cc_final: 0.8103 (mpt180) REVERT: C 306 PHE cc_start: 0.8443 (t80) cc_final: 0.7856 (t80) REVERT: D 9 MET cc_start: 0.8058 (mtp) cc_final: 0.7437 (ttm) REVERT: D 220 TYR cc_start: 0.8626 (t80) cc_final: 0.8394 (t80) REVERT: D 223 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8715 (pp) REVERT: D 244 TYR cc_start: 0.8767 (p90) cc_final: 0.8503 (p90) REVERT: D 286 MET cc_start: 0.8849 (mtm) cc_final: 0.8609 (mtm) REVERT: D 426 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.7996 (m-10) REVERT: E 142 LYS cc_start: 0.9453 (mttt) cc_final: 0.9241 (mttp) REVERT: E 147 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: E 170 LYS cc_start: 0.8815 (mttt) cc_final: 0.8614 (mtpm) REVERT: E 179 MET cc_start: 0.8888 (mpp) cc_final: 0.8588 (mpp) REVERT: E 210 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: E 256 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: E 308 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8732 (mtmp) REVERT: F 1 GLN cc_start: 0.8692 (mp10) cc_final: 0.8420 (mp10) REVERT: F 407 LEU cc_start: 0.9182 (mt) cc_final: 0.8801 (mm) REVERT: F 415 THR cc_start: 0.9224 (p) cc_final: 0.8850 (m) REVERT: F 426 GLN cc_start: 0.9081 (tt0) cc_final: 0.8809 (tt0) REVERT: F 433 GLU cc_start: 0.8966 (pt0) cc_final: 0.8674 (pt0) REVERT: F 459 ARG cc_start: 0.8115 (pmt170) cc_final: 0.7876 (ppt170) REVERT: F 470 MET cc_start: 0.8670 (mtm) cc_final: 0.8232 (mtt) REVERT: F 481 TYR cc_start: 0.7968 (m-80) cc_final: 0.7572 (m-80) REVERT: G 469 GLU cc_start: 0.7563 (mp0) cc_final: 0.7216 (mp0) outliers start: 59 outliers final: 20 residues processed: 301 average time/residue: 1.0634 time to fit residues: 359.9043 Evaluate side-chains 272 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 133 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 chunk 160 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 2 optimal weight: 0.0040 overall best weight: 1.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 77 HIS E 200 GLN E 227 ASN E 240 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059536 restraints weight = 125846.568| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 5.17 r_work: 0.2559 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16329 Z= 0.153 Angle : 0.626 11.476 22268 Z= 0.318 Chirality : 0.045 0.226 2548 Planarity : 0.004 0.051 2706 Dihedral : 8.369 72.420 2847 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.41 % Allowed : 14.93 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1889 helix: 2.24 (0.21), residues: 582 sheet: 0.89 (0.23), residues: 513 loop : 0.77 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 426 HIS 0.005 0.001 HIS E 240 PHE 0.019 0.002 PHE D 221 TYR 0.028 0.002 TYR C 299 ARG 0.005 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 13) link_NAG-ASN : angle 1.82926 ( 39) link_ALPHA1-6 : bond 0.00796 ( 4) link_ALPHA1-6 : angle 1.75772 ( 12) link_BETA1-4 : bond 0.00409 ( 11) link_BETA1-4 : angle 1.54510 ( 33) link_ALPHA1-3 : bond 0.01059 ( 4) link_ALPHA1-3 : angle 1.82541 ( 12) hydrogen bonds : bond 0.04575 ( 816) hydrogen bonds : angle 4.67027 ( 2552) SS BOND : bond 0.00263 ( 7) SS BOND : angle 0.42088 ( 14) covalent geometry : bond 0.00344 (16290) covalent geometry : angle 0.61699 (22158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8988 (mp0) REVERT: A 92 GLU cc_start: 0.8987 (pt0) cc_final: 0.8365 (pm20) REVERT: A 131 ASP cc_start: 0.9143 (p0) cc_final: 0.8605 (p0) REVERT: A 345 ASN cc_start: 0.8371 (m110) cc_final: 0.7905 (m110) REVERT: B 49 MET cc_start: 0.8478 (tmm) cc_final: 0.8133 (pp-130) REVERT: B 190 GLU cc_start: 0.8966 (tt0) cc_final: 0.8737 (pt0) REVERT: B 223 LEU cc_start: 0.9514 (tp) cc_final: 0.9260 (pp) REVERT: B 244 TYR cc_start: 0.8584 (p90) cc_final: 0.8250 (p90) REVERT: B 425 ARG cc_start: 0.8874 (ttt180) cc_final: 0.8122 (mpt180) REVERT: B 440 LEU cc_start: 0.8991 (tt) cc_final: 0.8762 (tp) REVERT: C 286 MET cc_start: 0.8319 (mmm) cc_final: 0.7708 (mtm) REVERT: C 298 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8832 (tm-30) REVERT: C 306 PHE cc_start: 0.8384 (t80) cc_final: 0.7682 (t80) REVERT: D 9 MET cc_start: 0.8146 (mtp) cc_final: 0.7661 (ttm) REVERT: D 95 ASP cc_start: 0.9087 (p0) cc_final: 0.8699 (p0) REVERT: D 181 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7826 (mm) REVERT: D 220 TYR cc_start: 0.8695 (t80) cc_final: 0.8330 (t80) REVERT: D 244 TYR cc_start: 0.8622 (p90) cc_final: 0.8414 (p90) REVERT: D 286 MET cc_start: 0.8885 (mtm) cc_final: 0.8671 (mtm) REVERT: D 426 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: E 142 LYS cc_start: 0.9441 (mttt) cc_final: 0.9234 (mttp) REVERT: E 147 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: E 179 MET cc_start: 0.8849 (mpp) cc_final: 0.8521 (mpp) REVERT: E 210 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: E 308 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8488 (mtmp) REVERT: F 407 LEU cc_start: 0.9156 (mt) cc_final: 0.8813 (mm) REVERT: F 415 THR cc_start: 0.9256 (p) cc_final: 0.8854 (m) REVERT: F 426 GLN cc_start: 0.9095 (tt0) cc_final: 0.8802 (tt0) REVERT: F 433 GLU cc_start: 0.8978 (pt0) cc_final: 0.8684 (pt0) REVERT: F 459 ARG cc_start: 0.8068 (pmt170) cc_final: 0.7809 (ppt170) REVERT: F 472 ASN cc_start: 0.8424 (m-40) cc_final: 0.8218 (m-40) REVERT: F 481 TYR cc_start: 0.8161 (m-80) cc_final: 0.7850 (m-80) REVERT: G 407 LEU cc_start: 0.8927 (mt) cc_final: 0.8693 (mp) REVERT: G 440 TRP cc_start: 0.8589 (m100) cc_final: 0.8238 (m100) REVERT: G 454 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7308 (ttp80) REVERT: G 460 ASP cc_start: 0.6388 (p0) cc_final: 0.6081 (OUTLIER) REVERT: G 469 GLU cc_start: 0.8161 (mp0) cc_final: 0.7750 (mp0) REVERT: G 504 GLN cc_start: 0.8616 (pm20) cc_final: 0.8402 (pm20) outliers start: 55 outliers final: 18 residues processed: 312 average time/residue: 1.1786 time to fit residues: 408.9427 Evaluate side-chains 283 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 441 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 165 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS C 64 GLN A C 243 ASN C 265 ASN D 265 ASN E 77 HIS E 227 ASN G 414 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.054564 restraints weight = 128124.769| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 5.07 r_work: 0.2470 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 16329 Z= 0.346 Angle : 0.732 10.964 22268 Z= 0.372 Chirality : 0.049 0.252 2548 Planarity : 0.004 0.043 2706 Dihedral : 8.511 75.151 2847 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.64 % Allowed : 16.25 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1889 helix: 2.23 (0.21), residues: 576 sheet: 0.76 (0.22), residues: 526 loop : 0.55 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 426 HIS 0.006 0.002 HIS E 135 PHE 0.027 0.002 PHE D 221 TYR 0.033 0.002 TYR C 299 ARG 0.006 0.001 ARG B 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 13) link_NAG-ASN : angle 2.26780 ( 39) link_ALPHA1-6 : bond 0.00445 ( 4) link_ALPHA1-6 : angle 1.76650 ( 12) link_BETA1-4 : bond 0.00545 ( 11) link_BETA1-4 : angle 2.02470 ( 33) link_ALPHA1-3 : bond 0.00572 ( 4) link_ALPHA1-3 : angle 2.05458 ( 12) hydrogen bonds : bond 0.04716 ( 816) hydrogen bonds : angle 4.81554 ( 2552) SS BOND : bond 0.00306 ( 7) SS BOND : angle 0.86195 ( 14) covalent geometry : bond 0.00795 (16290) covalent geometry : angle 0.72069 (22158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.9019 (mp0) REVERT: A 92 GLU cc_start: 0.8989 (pt0) cc_final: 0.8468 (pm20) REVERT: A 155 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8415 (mpp) REVERT: A 345 ASN cc_start: 0.8367 (m110) cc_final: 0.7920 (m110) REVERT: B 49 MET cc_start: 0.8532 (tmm) cc_final: 0.8170 (pp-130) REVERT: B 223 LEU cc_start: 0.9502 (tp) cc_final: 0.9162 (pp) REVERT: B 224 GLN cc_start: 0.9105 (tp40) cc_final: 0.8855 (tp40) REVERT: B 244 TYR cc_start: 0.8617 (p90) cc_final: 0.8368 (p90) REVERT: B 425 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8079 (mpt180) REVERT: C 227 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8732 (tpp) REVERT: C 255 ILE cc_start: 0.9504 (pp) cc_final: 0.9263 (pp) REVERT: C 286 MET cc_start: 0.8260 (mmm) cc_final: 0.7748 (mtt) REVERT: C 306 PHE cc_start: 0.8338 (t80) cc_final: 0.7684 (t80) REVERT: D 286 MET cc_start: 0.8946 (mtm) cc_final: 0.8663 (mtm) REVERT: D 426 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: E 114 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8583 (mmm-85) REVERT: E 142 LYS cc_start: 0.9451 (mttt) cc_final: 0.9236 (mttp) REVERT: E 170 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8669 (mttm) REVERT: E 179 MET cc_start: 0.8955 (mpp) cc_final: 0.8630 (mpp) REVERT: F 407 LEU cc_start: 0.9367 (mt) cc_final: 0.9038 (mm) REVERT: F 426 GLN cc_start: 0.9151 (tt0) cc_final: 0.8913 (tt0) REVERT: F 470 MET cc_start: 0.8566 (mtp) cc_final: 0.8305 (mtm) REVERT: F 472 ASN cc_start: 0.8881 (m-40) cc_final: 0.8679 (m-40) REVERT: G 407 LEU cc_start: 0.9020 (mt) cc_final: 0.8685 (mp) REVERT: G 440 TRP cc_start: 0.8773 (m100) cc_final: 0.8530 (m100) REVERT: G 469 GLU cc_start: 0.8195 (mp0) cc_final: 0.7708 (mp0) REVERT: G 470 MET cc_start: 0.8719 (mtm) cc_final: 0.7616 (mtm) REVERT: G 472 ASN cc_start: 0.8887 (m-40) cc_final: 0.8171 (t0) REVERT: G 476 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8692 (tp30) REVERT: G 504 GLN cc_start: 0.8471 (pm20) cc_final: 0.8250 (pm20) outliers start: 60 outliers final: 19 residues processed: 290 average time/residue: 1.1837 time to fit residues: 381.5276 Evaluate side-chains 272 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 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 114 ARG Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN B C 265 ASN E 43 ASN E 77 HIS E 213 GLN E 227 ASN G 414 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.057078 restraints weight = 118514.117| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 5.02 r_work: 0.2516 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16329 Z= 0.156 Angle : 0.633 9.235 22268 Z= 0.319 Chirality : 0.045 0.256 2548 Planarity : 0.004 0.037 2706 Dihedral : 7.713 68.415 2847 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.17 % Allowed : 16.55 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1889 helix: 2.31 (0.21), residues: 575 sheet: 0.74 (0.23), residues: 515 loop : 0.57 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 426 HIS 0.002 0.001 HIS C 267 PHE 0.019 0.002 PHE D 221 TYR 0.027 0.002 TYR B 299 ARG 0.005 0.000 ARG G 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 13) link_NAG-ASN : angle 1.91861 ( 39) link_ALPHA1-6 : bond 0.00779 ( 4) link_ALPHA1-6 : angle 1.77444 ( 12) link_BETA1-4 : bond 0.00362 ( 11) link_BETA1-4 : angle 1.58298 ( 33) link_ALPHA1-3 : bond 0.01045 ( 4) link_ALPHA1-3 : angle 1.80709 ( 12) hydrogen bonds : bond 0.04078 ( 816) hydrogen bonds : angle 4.56143 ( 2552) SS BOND : bond 0.00150 ( 7) SS BOND : angle 0.38188 ( 14) covalent geometry : bond 0.00355 (16290) covalent geometry : angle 0.62340 (22158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.9052 (mp0) REVERT: A 92 GLU cc_start: 0.9003 (pt0) cc_final: 0.8443 (pm20) REVERT: A 131 ASP cc_start: 0.9190 (p0) cc_final: 0.8645 (p0) REVERT: A 155 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8390 (mpp) REVERT: A 345 ASN cc_start: 0.8338 (m110) cc_final: 0.7895 (m110) REVERT: B 49 MET cc_start: 0.8598 (tmm) cc_final: 0.8206 (pp-130) REVERT: B 223 LEU cc_start: 0.9490 (tp) cc_final: 0.9162 (pp) REVERT: B 224 GLN cc_start: 0.9116 (tp40) cc_final: 0.8873 (tp40) REVERT: B 244 TYR cc_start: 0.8621 (p90) cc_final: 0.8340 (p90) REVERT: B 425 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8008 (mpt180) REVERT: C 190 GLU cc_start: 0.8805 (tt0) cc_final: 0.8554 (tt0) REVERT: C 255 ILE cc_start: 0.9470 (pp) cc_final: 0.9212 (pp) REVERT: C 286 MET cc_start: 0.8279 (mmm) cc_final: 0.7760 (mtt) REVERT: C 301 PHE cc_start: 0.8869 (t80) cc_final: 0.8374 (t80) REVERT: C 306 PHE cc_start: 0.8279 (t80) cc_final: 0.7565 (t80) REVERT: D 95 ASP cc_start: 0.9139 (p0) cc_final: 0.8723 (p0) REVERT: D 286 MET cc_start: 0.8925 (mtm) cc_final: 0.8636 (mtm) REVERT: D 426 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: E 142 LYS cc_start: 0.9408 (mttt) cc_final: 0.9197 (mttp) REVERT: E 147 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: E 179 MET cc_start: 0.8919 (mpp) cc_final: 0.8601 (mpp) REVERT: E 308 LYS cc_start: 0.8770 (mtmp) cc_final: 0.8368 (mtmp) REVERT: F 407 LEU cc_start: 0.9337 (mt) cc_final: 0.8999 (mm) REVERT: F 426 GLN cc_start: 0.9158 (tt0) cc_final: 0.8916 (tt0) REVERT: F 458 SER cc_start: 0.9021 (t) cc_final: 0.8631 (p) REVERT: F 469 GLU cc_start: 0.8472 (mp0) cc_final: 0.8075 (mp0) REVERT: F 470 MET cc_start: 0.8793 (mtp) cc_final: 0.8497 (mtm) REVERT: F 472 ASN cc_start: 0.8824 (m-40) cc_final: 0.8581 (m-40) REVERT: G 1 GLN cc_start: 0.8451 (mp10) cc_final: 0.7852 (pm20) REVERT: G 433 GLU cc_start: 0.8403 (pp20) cc_final: 0.8188 (pp20) REVERT: G 440 TRP cc_start: 0.8719 (m100) cc_final: 0.8276 (m100) REVERT: G 469 GLU cc_start: 0.8172 (mp0) cc_final: 0.7636 (mp0) REVERT: G 470 MET cc_start: 0.8678 (mtm) cc_final: 0.8343 (mtp) REVERT: G 472 ASN cc_start: 0.8985 (m-40) cc_final: 0.8176 (t0) REVERT: G 476 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8677 (tp30) REVERT: G 481 TYR cc_start: 0.8375 (m-10) cc_final: 0.8006 (m-80) REVERT: G 482 TYR cc_start: 0.9032 (m-80) cc_final: 0.8829 (m-10) REVERT: G 504 GLN cc_start: 0.8533 (pm20) cc_final: 0.8318 (pm20) outliers start: 52 outliers final: 22 residues processed: 291 average time/residue: 1.1520 time to fit residues: 373.7338 Evaluate side-chains 276 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 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 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN D 265 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 = 0.3332 r_free = 0.3332 target = 0.085614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.057195 restraints weight = 110561.272| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 4.83 r_work: 0.2524 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16329 Z= 0.168 Angle : 0.636 9.594 22268 Z= 0.319 Chirality : 0.046 0.312 2548 Planarity : 0.004 0.035 2706 Dihedral : 7.313 65.692 2847 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.29 % Allowed : 16.73 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1889 helix: 2.32 (0.21), residues: 575 sheet: 0.73 (0.23), residues: 521 loop : 0.51 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 426 HIS 0.005 0.001 HIS E 104 PHE 0.017 0.001 PHE A 291 TYR 0.028 0.002 TYR E 318 ARG 0.005 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 13) link_NAG-ASN : angle 2.08974 ( 39) link_ALPHA1-6 : bond 0.00848 ( 4) link_ALPHA1-6 : angle 1.78823 ( 12) link_BETA1-4 : bond 0.00407 ( 11) link_BETA1-4 : angle 1.60441 ( 33) link_ALPHA1-3 : bond 0.00918 ( 4) link_ALPHA1-3 : angle 1.86511 ( 12) hydrogen bonds : bond 0.03949 ( 816) hydrogen bonds : angle 4.47108 ( 2552) SS BOND : bond 0.00161 ( 7) SS BOND : angle 0.35124 ( 14) covalent geometry : bond 0.00383 (16290) covalent geometry : angle 0.62510 (22158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9041 (mp0) REVERT: A 92 GLU cc_start: 0.8989 (pt0) cc_final: 0.8463 (pm20) REVERT: A 155 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8401 (mpp) REVERT: A 319 MET cc_start: 0.9205 (ttp) cc_final: 0.8964 (ttm) REVERT: A 345 ASN cc_start: 0.8333 (m110) cc_final: 0.7881 (m110) REVERT: B 49 MET cc_start: 0.8676 (tmm) cc_final: 0.8279 (pp-130) REVERT: B 223 LEU cc_start: 0.9487 (tp) cc_final: 0.9184 (pp) REVERT: B 224 GLN cc_start: 0.9095 (tp40) cc_final: 0.8824 (tp40) REVERT: B 244 TYR cc_start: 0.8598 (p90) cc_final: 0.8377 (p90) REVERT: B 286 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7849 (mpp) REVERT: B 425 ARG cc_start: 0.8821 (ttt180) cc_final: 0.8002 (mpt180) REVERT: B 437 LEU cc_start: 0.8707 (tm) cc_final: 0.8334 (mp) REVERT: C 49 MET cc_start: 0.8267 (tmm) cc_final: 0.8028 (pp-130) REVERT: C 190 GLU cc_start: 0.8809 (tt0) cc_final: 0.8494 (tt0) REVERT: C 255 ILE cc_start: 0.9463 (pp) cc_final: 0.9230 (pp) REVERT: C 274 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8903 (mmmm) REVERT: C 286 MET cc_start: 0.8247 (mmm) cc_final: 0.7715 (mtm) REVERT: C 301 PHE cc_start: 0.8838 (t80) cc_final: 0.8210 (t80) REVERT: D 95 ASP cc_start: 0.9143 (p0) cc_final: 0.8713 (p0) REVERT: D 220 TYR cc_start: 0.8667 (t80) cc_final: 0.8378 (t80) REVERT: D 286 MET cc_start: 0.8923 (mtm) cc_final: 0.8623 (mtm) REVERT: D 426 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: E 142 LYS cc_start: 0.9400 (mttt) cc_final: 0.9198 (mttp) REVERT: E 147 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: E 170 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8650 (mttm) REVERT: E 179 MET cc_start: 0.8928 (mpp) cc_final: 0.8614 (mpp) REVERT: E 210 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: E 308 LYS cc_start: 0.8814 (mtmp) cc_final: 0.8413 (mtmp) REVERT: F 426 GLN cc_start: 0.9091 (tt0) cc_final: 0.8859 (tt0) REVERT: F 458 SER cc_start: 0.9033 (t) cc_final: 0.8655 (p) REVERT: F 469 GLU cc_start: 0.8560 (mp0) cc_final: 0.8119 (mp0) REVERT: F 470 MET cc_start: 0.8840 (mtp) cc_final: 0.8399 (mtm) REVERT: F 472 ASN cc_start: 0.8862 (m-40) cc_final: 0.8621 (m-40) REVERT: G 407 LEU cc_start: 0.8756 (mp) cc_final: 0.8550 (mt) REVERT: G 433 GLU cc_start: 0.8380 (pp20) cc_final: 0.8126 (pp20) REVERT: G 440 TRP cc_start: 0.8652 (m100) cc_final: 0.8338 (m100) REVERT: G 469 GLU cc_start: 0.8165 (mp0) cc_final: 0.7566 (mp0) REVERT: G 470 MET cc_start: 0.8639 (mtm) cc_final: 0.8252 (mtp) REVERT: G 472 ASN cc_start: 0.9076 (m-40) cc_final: 0.8411 (t0) REVERT: G 474 LYS cc_start: 0.8220 (mptt) cc_final: 0.7567 (mptm) REVERT: G 476 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8687 (tp30) REVERT: G 478 THR cc_start: 0.8880 (m) cc_final: 0.8610 (p) REVERT: G 504 GLN cc_start: 0.8542 (pm20) cc_final: 0.8305 (pm20) outliers start: 54 outliers final: 23 residues processed: 291 average time/residue: 1.1585 time to fit residues: 378.3299 Evaluate side-chains 288 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 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 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3344 r_free = 0.3344 target = 0.087034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.059126 restraints weight = 124310.373| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 5.08 r_work: 0.2547 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16329 Z= 0.124 Angle : 0.632 10.307 22268 Z= 0.311 Chirality : 0.045 0.337 2548 Planarity : 0.003 0.036 2706 Dihedral : 6.431 58.564 2847 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.87 % Allowed : 17.74 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 1889 helix: 2.30 (0.21), residues: 578 sheet: 0.73 (0.23), residues: 530 loop : 0.64 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 426 HIS 0.003 0.001 HIS E 104 PHE 0.017 0.001 PHE C 240 TYR 0.028 0.001 TYR E 318 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 13) link_NAG-ASN : angle 1.74552 ( 39) link_ALPHA1-6 : bond 0.01052 ( 4) link_ALPHA1-6 : angle 1.65707 ( 12) link_BETA1-4 : bond 0.00435 ( 11) link_BETA1-4 : angle 1.38588 ( 33) link_ALPHA1-3 : bond 0.01123 ( 4) link_ALPHA1-3 : angle 1.74097 ( 12) hydrogen bonds : bond 0.03636 ( 816) hydrogen bonds : angle 4.30701 ( 2552) SS BOND : bond 0.00135 ( 7) SS BOND : angle 0.26580 ( 14) covalent geometry : bond 0.00280 (16290) covalent geometry : angle 0.62401 (22158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8978 (mp0) REVERT: A 92 GLU cc_start: 0.9002 (pt0) cc_final: 0.8420 (pm20) REVERT: A 131 ASP cc_start: 0.9250 (p0) cc_final: 0.8629 (p0) REVERT: A 155 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8235 (mpp) REVERT: A 319 MET cc_start: 0.9159 (ttp) cc_final: 0.8917 (ttm) REVERT: A 345 ASN cc_start: 0.8370 (m110) cc_final: 0.7924 (m110) REVERT: B 49 MET cc_start: 0.8646 (tmm) cc_final: 0.8207 (pp-130) REVERT: B 223 LEU cc_start: 0.9499 (tp) cc_final: 0.9216 (pp) REVERT: B 224 GLN cc_start: 0.9040 (tp40) cc_final: 0.8810 (tp40) REVERT: B 244 TYR cc_start: 0.8642 (p90) cc_final: 0.8395 (p90) REVERT: B 286 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7741 (mpp) REVERT: B 425 ARG cc_start: 0.8826 (ttt180) cc_final: 0.7990 (mpt180) REVERT: B 437 LEU cc_start: 0.8679 (tm) cc_final: 0.8303 (mp) REVERT: C 49 MET cc_start: 0.8385 (tmm) cc_final: 0.8028 (ppp) REVERT: C 190 GLU cc_start: 0.8944 (tt0) cc_final: 0.8641 (tt0) REVERT: C 255 ILE cc_start: 0.9412 (pp) cc_final: 0.9188 (pp) REVERT: C 274 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8924 (mmmm) REVERT: C 286 MET cc_start: 0.8154 (mmm) cc_final: 0.7632 (mtm) REVERT: C 301 PHE cc_start: 0.8779 (t80) cc_final: 0.8190 (t80) REVERT: C 429 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8701 (mp) REVERT: D 95 ASP cc_start: 0.9090 (p0) cc_final: 0.8677 (p0) REVERT: D 220 TYR cc_start: 0.8615 (t80) cc_final: 0.8352 (t80) REVERT: D 286 MET cc_start: 0.8913 (mtm) cc_final: 0.8575 (mtm) REVERT: D 426 TRP cc_start: 0.8350 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: E 142 LYS cc_start: 0.9329 (mttt) cc_final: 0.9122 (mttp) REVERT: E 173 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.9065 (mpp) REVERT: E 179 MET cc_start: 0.8830 (mpp) cc_final: 0.8488 (mpp) REVERT: E 210 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8541 (mp10) REVERT: E 233 GLN cc_start: 0.8673 (mt0) cc_final: 0.8235 (tp40) REVERT: F 458 SER cc_start: 0.8997 (t) cc_final: 0.8615 (p) REVERT: F 469 GLU cc_start: 0.8671 (mp0) cc_final: 0.8196 (mp0) REVERT: F 470 MET cc_start: 0.8871 (mtp) cc_final: 0.8567 (mtm) REVERT: F 473 LEU cc_start: 0.8794 (tt) cc_final: 0.8293 (mp) REVERT: F 501 TYR cc_start: 0.9044 (m-80) cc_final: 0.8801 (m-80) REVERT: G 1 GLN cc_start: 0.8415 (mp10) cc_final: 0.8004 (pm20) REVERT: G 407 LEU cc_start: 0.8732 (mp) cc_final: 0.8528 (mt) REVERT: G 433 GLU cc_start: 0.8434 (pp20) cc_final: 0.8167 (pp20) REVERT: G 440 TRP cc_start: 0.8480 (m100) cc_final: 0.8265 (m100) REVERT: G 459 ARG cc_start: 0.8385 (ppt90) cc_final: 0.7928 (ptt-90) REVERT: G 464 ASN cc_start: 0.9026 (m-40) cc_final: 0.8824 (m-40) REVERT: G 469 GLU cc_start: 0.8175 (mp0) cc_final: 0.7539 (mp0) REVERT: G 470 MET cc_start: 0.8628 (mtm) cc_final: 0.8260 (mtp) REVERT: G 472 ASN cc_start: 0.9108 (m-40) cc_final: 0.8394 (t0) REVERT: G 474 LYS cc_start: 0.8253 (mptt) cc_final: 0.7682 (mptm) REVERT: G 476 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8687 (tp30) REVERT: G 478 THR cc_start: 0.8986 (m) cc_final: 0.8731 (p) REVERT: G 504 GLN cc_start: 0.8561 (pm20) cc_final: 0.8323 (pm20) outliers start: 47 outliers final: 17 residues processed: 296 average time/residue: 1.0565 time to fit residues: 351.1482 Evaluate side-chains 290 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 210 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0388 > 50: distance: 32 - 199: 6.939 distance: 35 - 196: 14.061 distance: 94 - 155: 21.676 distance: 97 - 152: 7.238 distance: 107 - 136: 17.055 distance: 127 - 133: 9.778 distance: 133 - 134: 9.889 distance: 134 - 135: 5.637 distance: 134 - 137: 13.916 distance: 135 - 136: 15.784 distance: 135 - 141: 7.371 distance: 137 - 138: 19.665 distance: 137 - 139: 8.090 distance: 138 - 140: 8.511 distance: 141 - 142: 6.156 distance: 141 - 206: 12.415 distance: 142 - 143: 7.958 distance: 142 - 145: 6.168 distance: 143 - 144: 16.287 distance: 143 - 152: 6.891 distance: 144 - 203: 16.646 distance: 145 - 146: 7.568 distance: 148 - 149: 6.143 distance: 149 - 150: 3.922 distance: 149 - 151: 3.357 distance: 152 - 153: 7.129 distance: 153 - 154: 23.611 distance: 153 - 156: 6.526 distance: 154 - 155: 13.181 distance: 154 - 160: 49.528 distance: 156 - 157: 6.677 distance: 157 - 158: 3.840 distance: 157 - 159: 7.414 distance: 160 - 161: 50.039 distance: 161 - 162: 34.510 distance: 161 - 164: 39.882 distance: 162 - 163: 13.613 distance: 162 - 170: 19.991 distance: 164 - 165: 17.779 distance: 165 - 166: 20.191 distance: 165 - 167: 15.826 distance: 166 - 168: 18.143 distance: 167 - 169: 15.009 distance: 168 - 169: 14.795 distance: 170 - 171: 7.579 distance: 170 - 176: 10.514 distance: 171 - 172: 10.203 distance: 171 - 174: 4.293 distance: 172 - 173: 13.760 distance: 172 - 177: 13.739 distance: 174 - 175: 6.720 distance: 175 - 176: 4.697 distance: 177 - 178: 12.417 distance: 178 - 179: 7.426 distance: 178 - 181: 10.320 distance: 179 - 180: 21.305 distance: 179 - 185: 17.810 distance: 181 - 182: 13.460 distance: 182 - 183: 5.225 distance: 182 - 184: 17.907 distance: 185 - 186: 20.946 distance: 186 - 187: 11.804 distance: 187 - 188: 7.898 distance: 187 - 189: 6.381 distance: 189 - 190: 6.927 distance: 190 - 191: 8.674 distance: 190 - 193: 7.957 distance: 191 - 192: 5.791 distance: 191 - 196: 14.131 distance: 193 - 194: 5.565 distance: 193 - 195: 4.263 distance: 196 - 197: 16.152 distance: 197 - 198: 13.510 distance: 197 - 200: 4.721 distance: 198 - 199: 4.996 distance: 198 - 203: 11.541 distance: 200 - 201: 9.828 distance: 200 - 202: 14.239 distance: 203 - 204: 6.759 distance: 204 - 205: 7.588 distance: 204 - 207: 10.427 distance: 205 - 206: 6.177 distance: 205 - 211: 12.363 distance: 207 - 208: 8.065 distance: 208 - 209: 13.825 distance: 208 - 210: 9.459