Starting phenix.real_space_refine on Tue Aug 26 11:13:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9awk_43926/08_2025/9awk_43926_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9awk_43926/08_2025/9awk_43926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9awk_43926/08_2025/9awk_43926_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9awk_43926/08_2025/9awk_43926_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9awk_43926/08_2025/9awk_43926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9awk_43926/08_2025/9awk_43926.map" } resolution = 2.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 100 5.16 5 C 11750 2.51 5 N 2868 2.21 5 O 3386 1.98 5 H 17450 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35561 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6508 Classifications: {'peptide': 402} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 380} Chain breaks: 1 Chain: "E" Number of atoms: 6670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6670 Classifications: {'peptide': 410} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 382} Chain breaks: 2 Chain: "C" Number of atoms: 6501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6501 Classifications: {'peptide': 401} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 379} Chain breaks: 1 Chain: "D" Number of atoms: 6949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 6949 Classifications: {'peptide': 429} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 398} Chain breaks: 1 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 942 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "G" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 951 Classifications: {'peptide': 62} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "B" Number of atoms: 6325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6325 Classifications: {'peptide': 396} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "I" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" 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: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N POV A 501 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV A 501 " occ=0.75 residue: pdb=" N POV E 601 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 601 " occ=0.75 residue: pdb=" N POV E 602 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 602 " occ=0.75 residue: pdb=" N POV E 603 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 603 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" N POV D 601 " occ=0.75 ... (45 atoms not shown) pdb="C316 POV D 601 " occ=0.75 Time building chain proxies: 5.53, per 1000 atoms: 0.16 Number of scatterers: 35561 At special positions: 0 Unit cell: (100.98, 131.835, 175.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 7 15.00 O 3386 8.00 N 2868 7.00 C 11750 6.00 H 17450 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 52 " distance=2.04 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 17 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 22 " distance=2.04 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " 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 ALPHA1-2 " MAN I 5 " - " MAN I 6 " " MAN I 7 " - " MAN I 8 " " MAN I 9 " - " MAN I 10 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN K 10 " - " MAN K 11 " ALPHA1-3 " BMA I 3 " - " MAN I 9 " " MAN I 4 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA L 3 " - " MAN L 6 " " MAN L 4 " - " MAN L 5 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 7 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 10 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " BETA1-4 " 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG D 602 " - " ASN D 96 " " NAG I 1 " - " ASN A 161 " " NAG J 1 " - " ASN E 165 " " NAG K 1 " - " ASN C 161 " " NAG L 1 " - " ASN D 163 " " NAG M 1 " - " ASN B 163 " " NAG N 1 " - " ASN B 52 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 893.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 23 sheets defined 40.9% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.129A pdb=" N GLY A 93 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 238 through 251 removed outlier: 4.076A pdb=" N GLY A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.952A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 320 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 389 through 457 removed outlier: 3.609A pdb=" N ALA A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.873A pdb=" N SER E 90 " --> pdb=" O TYR E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 246 through 253 Processing helix chain 'E' and resid 253 through 266 Processing helix chain 'E' and resid 267 through 270 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 276 through 297 removed outlier: 3.593A pdb=" N LEU E 280 " --> pdb=" O GLU E 276 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 335 Processing helix chain 'E' and resid 344 through 352 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.780A pdb=" N TYR E 358 " --> pdb=" O LYS E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 496 removed outlier: 3.790A pdb=" N GLU E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 88 through 93 removed outlier: 4.183A pdb=" N GLY C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 238 through 250 removed outlier: 3.986A pdb=" N GLY C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.874A pdb=" N LEU C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 320 Processing helix chain 'C' and resid 329 through 337 removed outlier: 3.600A pdb=" N ILE C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 455 removed outlier: 3.682A pdb=" N TRP C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 445 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ARG C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 262 through 268 removed outlier: 3.774A pdb=" N VAL D 266 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 267 " --> pdb=" O ASN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 296 removed outlier: 4.085A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 334 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.830A pdb=" N GLU D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 493 removed outlier: 3.548A pdb=" N GLU D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Proline residue: D 436 - end of helix Proline residue: D 478 - end of helix removed outlier: 3.653A pdb=" N GLN D 490 " --> pdb=" O TRP D 486 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 85 through 88 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.997A pdb=" N GLY B 95 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.965A pdb=" N ALA B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 removed outlier: 3.623A pdb=" N TYR B 263 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 293 removed outlier: 3.923A pdb=" N LYS B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 331 Processing helix chain 'B' and resid 439 through 499 removed outlier: 3.545A pdb=" N GLU B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.143A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY A 134 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.143A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY A 134 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A 69 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A 63 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 71 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG A 75 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU A 57 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 77 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A 55 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN A 79 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A 53 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N VAL A 81 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 51 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N TYR A 83 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 12.996A pdb=" N VAL A 49 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.828A pdb=" N THR A 168 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 219 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 200 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN A 228 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A 198 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 101 through 105 removed outlier: 4.060A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 101 through 105 removed outlier: 4.060A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU E 73 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU E 67 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER E 75 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR E 79 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU E 61 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP E 81 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU E 59 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU E 83 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE E 57 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL E 55 " --> pdb=" O THR E 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.912A pdb=" N ILE E 241 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.249A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.249A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 69 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL C 63 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR C 71 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 77 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU C 55 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN C 79 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL C 53 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N VAL C 81 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL C 51 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.778A pdb=" N THR C 168 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 219 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN C 228 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 198 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.963A pdb=" N ASN D 75 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TRP D 77 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLU D 79 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR D 58 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY D 81 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ALA D 56 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR D 83 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N SER D 54 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 51 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N SER D 181 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE D 53 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.402A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE D 240 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.402A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AB7, first strand: chain 'F' and resid 1 through 4 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AB9, first strand: chain 'G' and resid 1 through 4 Processing sheet with id=AC1, first strand: chain 'G' and resid 33 through 39 Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.810A pdb=" N ALA B 71 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER B 64 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 73 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN B 75 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS B 83 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN B 52 " --> pdb=" O CYS B 83 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 51 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN B 181 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.872A pdb=" N SER B 170 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN B 229 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU B 236 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.872A pdb=" N SER B 170 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN B 229 " --> pdb=" O SER B 170 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.92 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17422 1.04 - 1.24: 2029 1.24 - 1.44: 5828 1.44 - 1.64: 10583 1.64 - 1.84: 150 Bond restraints: 36012 Sorted by residual: bond pdb=" N PRO C 217 " pdb=" CD PRO C 217 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.67e+01 bond pdb=" NZ LYS B 465 " pdb=" HZ2 LYS B 465 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS A 388 " pdb=" HZ3 LYS A 388 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 165 " pdb=" HZ1 LYS C 165 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 334 " pdb=" HZ3 LYS A 334 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 36007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.53: 64965 11.53 - 23.05: 1 23.05 - 34.58: 0 34.58 - 46.10: 0 46.10 - 57.63: 1 Bond angle restraints: 64967 Sorted by residual: angle pdb=" CA ALA D 426 " pdb=" N ALA D 426 " pdb=" H ALA D 426 " ideal model delta sigma weight residual 114.00 171.63 -57.63 3.00e+00 1.11e-01 3.69e+02 angle pdb=" CA ARG E 232 " pdb=" N ARG E 232 " pdb=" H ARG E 232 " ideal model delta sigma weight residual 114.00 96.17 17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" N PHE A 345 " pdb=" CA PHE A 345 " pdb=" C PHE A 345 " ideal model delta sigma weight residual 112.34 105.73 6.61 1.30e+00 5.92e-01 2.58e+01 angle pdb=" N ASN C 342 " pdb=" CA ASN C 342 " pdb=" C ASN C 342 " ideal model delta sigma weight residual 111.71 106.34 5.37 1.15e+00 7.56e-01 2.18e+01 angle pdb=" CA ARG E 149 " pdb=" C ARG E 149 " pdb=" O ARG E 149 " ideal model delta sigma weight residual 120.46 115.86 4.60 1.07e+00 8.73e-01 1.85e+01 ... (remaining 64962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 16663 28.14 - 56.28: 828 56.28 - 84.41: 123 84.41 - 112.55: 33 112.55 - 140.69: 5 Dihedral angle restraints: 17652 sinusoidal: 9975 harmonic: 7677 Sorted by residual: dihedral pdb=" CD ARG E 149 " pdb=" NE ARG E 149 " pdb=" CZ ARG E 149 " pdb=" NH1 ARG E 149 " ideal model delta sinusoidal sigma weight residual 0.00 -81.38 81.38 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS G 3 " pdb=" SG CYS G 3 " pdb=" SG CYS G 17 " pdb=" CB CYS G 17 " ideal model delta sinusoidal sigma weight residual -86.00 -132.71 46.71 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CD ARG E 233 " pdb=" NE ARG E 233 " pdb=" CZ ARG E 233 " pdb=" NH1 ARG E 233 " ideal model delta sinusoidal sigma weight residual 0.00 -37.40 37.40 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2992 0.336 - 0.671: 4 0.671 - 1.007: 2 1.007 - 1.343: 1 1.343 - 1.679: 1 Chirality restraints: 3000 Sorted by residual: chirality pdb=" C1 MAN I 4 " pdb=" O6 BMA I 3 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.79e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.49e+02 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.66e+02 ... (remaining 2997 not shown) Planarity restraints: 5105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.232 2.00e-02 2.50e+03 1.93e-01 4.65e+02 pdb=" C7 NAG N 2 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.318 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 149 " -1.124 9.50e-02 1.11e+02 3.75e-01 1.48e+02 pdb=" NE ARG E 149 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG E 149 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG E 149 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 149 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 149 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG E 149 " -0.016 2.00e-02 2.50e+03 pdb="HH21 ARG E 149 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG E 149 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " 0.127 2.00e-02 2.50e+03 1.07e-01 1.44e+02 pdb=" C7 NAG L 2 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " -0.173 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.102 2.00e-02 2.50e+03 ... (remaining 5102 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 375 2.05 - 2.69: 52402 2.69 - 3.32: 102449 3.32 - 3.96: 139864 3.96 - 4.60: 213245 Nonbonded interactions: 508335 Sorted by model distance: nonbonded pdb=" HH TYR B 37 " pdb=" H TRP B 108 " model vdw 1.411 2.100 nonbonded pdb="HD21 ASN C 161 " pdb=" O5 NAG K 1 " model vdw 1.452 1.960 nonbonded pdb=" OE2 GLU E 455 " pdb=" HD1 HIS D 447 " model vdw 1.491 2.450 nonbonded pdb="HD21 ASN A 161 " pdb=" O5 NAG I 1 " model vdw 1.497 1.960 nonbonded pdb=" HH TYR E 39 " pdb=" H TRP E 110 " model vdw 1.520 2.100 ... (remaining 508330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 456 or (resid 501 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or n \ ame O31 or name O32 or name P )))) selection = (chain 'C' and (resid 21 through 456 or resid 502)) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 0 through 60) } ncs_group { reference = (chain 'I' and (resid 1 or resid 4 through 10)) selection = (chain 'K' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'J' selection = chain 'M' } 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=0.75 max=1.00 mean=1.00 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: 12.240 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: 0.180 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.520 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.007 0.320 18615 Z= 0.344 Angle : 0.995 41.235 25416 Z= 0.473 Chirality : 0.070 1.679 3000 Planarity : 0.014 0.489 3078 Dihedral : 18.084 140.688 7441 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.30 % Allowed : 15.51 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2135 helix: 1.84 (0.18), residues: 774 sheet: 0.24 (0.23), residues: 465 loop : -0.40 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 466 TYR 0.026 0.002 TYR D 268 PHE 0.023 0.002 PHE A 345 TRP 0.020 0.001 TRP A 331 HIS 0.010 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00588 (18562) covalent geometry : angle 0.89392 (25272) SS BOND : bond 0.00476 ( 15) SS BOND : angle 2.01211 ( 30) hydrogen bonds : bond 0.11614 ( 878) hydrogen bonds : angle 5.43609 ( 2769) link_ALPHA1-2 : bond 0.00355 ( 7) link_ALPHA1-2 : angle 2.23530 ( 21) link_ALPHA1-3 : bond 0.01115 ( 6) link_ALPHA1-3 : angle 2.73618 ( 18) link_ALPHA1-6 : bond 0.00621 ( 7) link_ALPHA1-6 : angle 2.87263 ( 21) link_BETA1-4 : bond 0.01104 ( 11) link_BETA1-4 : angle 3.99924 ( 33) link_NAG-ASN : bond 0.19918 ( 7) link_NAG-ASN : angle 13.65943 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 LYS cc_start: 0.8488 (mttt) cc_final: 0.8250 (mttm) REVERT: B 224 GLU cc_start: 0.6978 (pm20) cc_final: 0.6688 (pm20) outliers start: 6 outliers final: 4 residues processed: 232 average time/residue: 1.2460 time to fit residues: 322.6971 Evaluate side-chains 210 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain B residue 309 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 452 ASN B 75 ASN B 176 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091016 restraints weight = 61402.474| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.87 r_work: 0.3052 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18615 Z= 0.153 Angle : 0.928 42.548 25416 Z= 0.381 Chirality : 0.047 0.378 3000 Planarity : 0.006 0.203 3078 Dihedral : 13.043 126.535 3269 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.31 % Allowed : 14.14 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2135 helix: 2.37 (0.18), residues: 774 sheet: 0.28 (0.22), residues: 472 loop : -0.14 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 149 TYR 0.012 0.001 TYR B 139 PHE 0.015 0.001 PHE B 194 TRP 0.009 0.001 TRP A 331 HIS 0.009 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00350 (18562) covalent geometry : angle 0.61272 (25272) SS BOND : bond 0.00464 ( 15) SS BOND : angle 1.18865 ( 30) hydrogen bonds : bond 0.04868 ( 878) hydrogen bonds : angle 4.38449 ( 2769) link_ALPHA1-2 : bond 0.00289 ( 7) link_ALPHA1-2 : angle 1.97042 ( 21) link_ALPHA1-3 : bond 0.00540 ( 6) link_ALPHA1-3 : angle 2.03885 ( 18) link_ALPHA1-6 : bond 0.00460 ( 7) link_ALPHA1-6 : angle 1.89363 ( 21) link_BETA1-4 : bond 0.00449 ( 11) link_BETA1-4 : angle 2.43960 ( 33) link_NAG-ASN : bond 0.00327 ( 7) link_NAG-ASN : angle 23.83393 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: A 328 MET cc_start: 0.7829 (tpt) cc_final: 0.7493 (tpt) REVERT: A 413 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7205 (t0) REVERT: C 449 ARG cc_start: 0.6930 (tpt170) cc_final: 0.6721 (tpt170) REVERT: F 43 LYS cc_start: 0.8097 (tptp) cc_final: 0.7803 (mptm) REVERT: G 54 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7582 (mtt-85) REVERT: G 57 LYS cc_start: 0.8552 (mttt) cc_final: 0.8320 (mttp) outliers start: 26 outliers final: 11 residues processed: 225 average time/residue: 1.1601 time to fit residues: 292.2897 Evaluate side-chains 211 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 309 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 173 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 138 optimal weight: 0.0370 chunk 175 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 111 optimal weight: 0.9990 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN C 237 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091316 restraints weight = 61049.077| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.87 r_work: 0.3054 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18615 Z= 0.116 Angle : 0.870 41.050 25416 Z= 0.351 Chirality : 0.046 0.401 3000 Planarity : 0.004 0.052 3078 Dihedral : 11.379 121.180 3262 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.06 % Allowed : 13.99 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2135 helix: 2.75 (0.18), residues: 778 sheet: 0.26 (0.22), residues: 481 loop : -0.05 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 297 TYR 0.011 0.001 TYR B 139 PHE 0.015 0.001 PHE A 346 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00257 (18562) covalent geometry : angle 0.54776 (25272) SS BOND : bond 0.00493 ( 15) SS BOND : angle 1.11535 ( 30) hydrogen bonds : bond 0.04472 ( 878) hydrogen bonds : angle 4.12776 ( 2769) link_ALPHA1-2 : bond 0.00207 ( 7) link_ALPHA1-2 : angle 1.70197 ( 21) link_ALPHA1-3 : bond 0.00681 ( 6) link_ALPHA1-3 : angle 1.45391 ( 18) link_ALPHA1-6 : bond 0.00711 ( 7) link_ALPHA1-6 : angle 1.65552 ( 21) link_BETA1-4 : bond 0.00469 ( 11) link_BETA1-4 : angle 2.20496 ( 33) link_NAG-ASN : bond 0.00493 ( 7) link_NAG-ASN : angle 23.18059 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: A 287 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7280 (m) REVERT: A 413 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.6779 (m110) REVERT: D 206 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: D 242 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7691 (ttm-80) REVERT: F 43 LYS cc_start: 0.8103 (tptp) cc_final: 0.7848 (mptm) REVERT: G 1 MET cc_start: 0.8278 (ttp) cc_final: 0.8058 (ttp) REVERT: G 54 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7643 (mtt-85) REVERT: G 57 LYS cc_start: 0.8599 (mttt) cc_final: 0.8375 (mttp) REVERT: B 469 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7356 (mp) REVERT: B 476 ARG cc_start: 0.7590 (tmt170) cc_final: 0.7243 (tpp80) outliers start: 21 outliers final: 4 residues processed: 218 average time/residue: 1.2551 time to fit residues: 304.3678 Evaluate side-chains 207 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 6 optimal weight: 0.0980 chunk 142 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088918 restraints weight = 60659.846| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.86 r_work: 0.3017 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18615 Z= 0.149 Angle : 0.878 42.280 25416 Z= 0.357 Chirality : 0.046 0.466 3000 Planarity : 0.004 0.043 3078 Dihedral : 10.870 113.304 3261 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.41 % Allowed : 13.43 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.18), residues: 2135 helix: 2.83 (0.18), residues: 778 sheet: 0.38 (0.23), residues: 475 loop : 0.04 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.012 0.001 TYR C 92 PHE 0.019 0.002 PHE B 194 TRP 0.009 0.001 TRP D 196 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00343 (18562) covalent geometry : angle 0.55341 (25272) SS BOND : bond 0.00491 ( 15) SS BOND : angle 1.21627 ( 30) hydrogen bonds : bond 0.04563 ( 878) hydrogen bonds : angle 4.10693 ( 2769) link_ALPHA1-2 : bond 0.00309 ( 7) link_ALPHA1-2 : angle 2.13737 ( 21) link_ALPHA1-3 : bond 0.00539 ( 6) link_ALPHA1-3 : angle 1.70659 ( 18) link_ALPHA1-6 : bond 0.00732 ( 7) link_ALPHA1-6 : angle 1.69132 ( 21) link_BETA1-4 : bond 0.00383 ( 11) link_BETA1-4 : angle 2.16009 ( 33) link_NAG-ASN : bond 0.00294 ( 7) link_NAG-ASN : angle 23.32410 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6816 (tp30) REVERT: A 413 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.6749 (m110) REVERT: C 149 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: D 242 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7773 (ttm-80) REVERT: F 43 LYS cc_start: 0.8100 (tptp) cc_final: 0.7862 (mptm) REVERT: G 1 MET cc_start: 0.8361 (ttp) cc_final: 0.8095 (ttp) REVERT: G 54 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7657 (mtt-85) REVERT: G 57 LYS cc_start: 0.8655 (mttt) cc_final: 0.8415 (mttm) REVERT: B 469 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7181 (mp) REVERT: B 476 ARG cc_start: 0.7501 (tmt170) cc_final: 0.7197 (tpp80) outliers start: 28 outliers final: 10 residues processed: 217 average time/residue: 1.2787 time to fit residues: 308.1082 Evaluate side-chains 209 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 111 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 HIS D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088833 restraints weight = 60444.025| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.86 r_work: 0.3021 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18615 Z= 0.135 Angle : 0.869 42.646 25416 Z= 0.353 Chirality : 0.046 0.447 3000 Planarity : 0.004 0.041 3078 Dihedral : 10.638 107.823 3261 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.26 % Allowed : 13.59 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.18), residues: 2135 helix: 2.91 (0.18), residues: 780 sheet: 0.34 (0.22), residues: 478 loop : 0.09 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 501 TYR 0.012 0.001 TYR C 92 PHE 0.016 0.001 PHE B 194 TRP 0.009 0.001 TRP D 196 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00307 (18562) covalent geometry : angle 0.53917 (25272) SS BOND : bond 0.00470 ( 15) SS BOND : angle 1.31282 ( 30) hydrogen bonds : bond 0.04469 ( 878) hydrogen bonds : angle 4.07221 ( 2769) link_ALPHA1-2 : bond 0.00176 ( 7) link_ALPHA1-2 : angle 1.96279 ( 21) link_ALPHA1-3 : bond 0.00602 ( 6) link_ALPHA1-3 : angle 1.53671 ( 18) link_ALPHA1-6 : bond 0.00743 ( 7) link_ALPHA1-6 : angle 1.68130 ( 21) link_BETA1-4 : bond 0.00390 ( 11) link_BETA1-4 : angle 2.09088 ( 33) link_NAG-ASN : bond 0.00311 ( 7) link_NAG-ASN : angle 23.39033 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6826 (tp30) REVERT: A 287 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.7123 (m) REVERT: A 413 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.6748 (m110) REVERT: C 149 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: D 242 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7741 (ttm-80) REVERT: D 321 MET cc_start: 0.8188 (mtp) cc_final: 0.7939 (mtt) REVERT: F 43 LYS cc_start: 0.8091 (tptp) cc_final: 0.7859 (mptm) REVERT: G 1 MET cc_start: 0.8344 (ttp) cc_final: 0.8084 (ttp) REVERT: G 54 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7648 (mtt-85) REVERT: G 57 LYS cc_start: 0.8643 (mttt) cc_final: 0.8411 (mttp) REVERT: B 469 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7242 (mp) REVERT: B 476 ARG cc_start: 0.7542 (tmt170) cc_final: 0.7243 (tpp80) outliers start: 25 outliers final: 8 residues processed: 215 average time/residue: 1.2131 time to fit residues: 290.2271 Evaluate side-chains 209 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN B 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.088294 restraints weight = 60200.839| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.86 r_work: 0.3002 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18615 Z= 0.156 Angle : 0.876 42.978 25416 Z= 0.359 Chirality : 0.047 0.466 3000 Planarity : 0.004 0.040 3078 Dihedral : 10.605 104.791 3259 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.57 % Allowed : 13.38 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.18), residues: 2135 helix: 2.91 (0.18), residues: 780 sheet: 0.43 (0.23), residues: 472 loop : 0.10 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.012 0.001 TYR C 92 PHE 0.017 0.002 PHE B 194 TRP 0.010 0.001 TRP D 196 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00361 (18562) covalent geometry : angle 0.54966 (25272) SS BOND : bond 0.00966 ( 15) SS BOND : angle 1.56671 ( 30) hydrogen bonds : bond 0.04586 ( 878) hydrogen bonds : angle 4.08181 ( 2769) link_ALPHA1-2 : bond 0.00262 ( 7) link_ALPHA1-2 : angle 2.10245 ( 21) link_ALPHA1-3 : bond 0.00563 ( 6) link_ALPHA1-3 : angle 1.59342 ( 18) link_ALPHA1-6 : bond 0.00736 ( 7) link_ALPHA1-6 : angle 1.68804 ( 21) link_BETA1-4 : bond 0.00425 ( 11) link_BETA1-4 : angle 2.13567 ( 33) link_NAG-ASN : bond 0.00264 ( 7) link_NAG-ASN : angle 23.35754 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6882 (tp30) REVERT: A 287 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7130 (m) REVERT: C 149 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: C 293 LEU cc_start: 0.8491 (tp) cc_final: 0.8272 (tt) REVERT: D 242 ARG cc_start: 0.8375 (ttm110) cc_final: 0.8094 (ttm110) REVERT: D 321 MET cc_start: 0.8197 (mtp) cc_final: 0.7942 (mtt) REVERT: F 43 LYS cc_start: 0.8073 (tptp) cc_final: 0.7846 (mptm) REVERT: G 1 MET cc_start: 0.8380 (ttp) cc_final: 0.8090 (ttp) REVERT: G 54 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7695 (mtt-85) REVERT: G 57 LYS cc_start: 0.8582 (mttt) cc_final: 0.8347 (mttp) REVERT: B 469 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7219 (mp) REVERT: B 476 ARG cc_start: 0.7561 (tmt170) cc_final: 0.7265 (tpp80) outliers start: 31 outliers final: 15 residues processed: 217 average time/residue: 1.2696 time to fit residues: 308.6853 Evaluate side-chains 216 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 47 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087778 restraints weight = 60408.845| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.86 r_work: 0.2992 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 18615 Z= 0.164 Angle : 0.881 43.359 25416 Z= 0.363 Chirality : 0.047 0.473 3000 Planarity : 0.004 0.039 3078 Dihedral : 10.622 103.894 3259 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.31 % Allowed : 13.54 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.18), residues: 2135 helix: 2.94 (0.18), residues: 780 sheet: 0.41 (0.23), residues: 476 loop : 0.11 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.013 0.001 TYR C 92 PHE 0.018 0.002 PHE B 194 TRP 0.011 0.001 TRP D 196 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00381 (18562) covalent geometry : angle 0.55598 (25272) SS BOND : bond 0.00974 ( 15) SS BOND : angle 2.00272 ( 30) hydrogen bonds : bond 0.04646 ( 878) hydrogen bonds : angle 4.09786 ( 2769) link_ALPHA1-2 : bond 0.00280 ( 7) link_ALPHA1-2 : angle 2.12532 ( 21) link_ALPHA1-3 : bond 0.00526 ( 6) link_ALPHA1-3 : angle 1.55290 ( 18) link_ALPHA1-6 : bond 0.00765 ( 7) link_ALPHA1-6 : angle 1.75087 ( 21) link_BETA1-4 : bond 0.00450 ( 11) link_BETA1-4 : angle 2.16163 ( 33) link_NAG-ASN : bond 0.00276 ( 7) link_NAG-ASN : angle 23.34661 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: A 287 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7155 (m) REVERT: C 149 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: D 242 ARG cc_start: 0.8375 (ttm110) cc_final: 0.7615 (ttm-80) REVERT: D 488 PHE cc_start: 0.8611 (m-80) cc_final: 0.8411 (m-80) REVERT: G 1 MET cc_start: 0.8323 (ttp) cc_final: 0.7991 (ttp) REVERT: G 54 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: G 57 LYS cc_start: 0.8571 (mttt) cc_final: 0.8278 (mtmm) REVERT: B 222 PRO cc_start: 0.7825 (Cg_exo) cc_final: 0.7580 (Cg_endo) REVERT: B 476 ARG cc_start: 0.7561 (tmt170) cc_final: 0.7273 (tpp80) outliers start: 26 outliers final: 11 residues processed: 214 average time/residue: 1.3736 time to fit residues: 327.9647 Evaluate side-chains 209 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 331 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.084993 restraints weight = 59723.212| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.87 r_work: 0.2958 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18615 Z= 0.210 Angle : 0.900 43.666 25416 Z= 0.378 Chirality : 0.049 0.517 3000 Planarity : 0.005 0.047 3078 Dihedral : 10.869 103.367 3259 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.41 % Allowed : 13.43 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.18), residues: 2135 helix: 2.82 (0.18), residues: 780 sheet: 0.38 (0.23), residues: 482 loop : 0.07 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.013 0.002 TYR C 92 PHE 0.020 0.002 PHE B 194 TRP 0.014 0.001 TRP D 196 HIS 0.005 0.001 HIS C 23 Details of bonding type rmsd covalent geometry : bond 0.00489 (18562) covalent geometry : angle 0.59145 (25272) SS BOND : bond 0.01476 ( 15) SS BOND : angle 1.99329 ( 30) hydrogen bonds : bond 0.04945 ( 878) hydrogen bonds : angle 4.20708 ( 2769) link_ALPHA1-2 : bond 0.00428 ( 7) link_ALPHA1-2 : angle 2.34564 ( 21) link_ALPHA1-3 : bond 0.00458 ( 6) link_ALPHA1-3 : angle 1.62290 ( 18) link_ALPHA1-6 : bond 0.00692 ( 7) link_ALPHA1-6 : angle 1.84239 ( 21) link_BETA1-4 : bond 0.00540 ( 11) link_BETA1-4 : angle 2.27034 ( 33) link_NAG-ASN : bond 0.00305 ( 7) link_NAG-ASN : angle 23.11060 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: A 287 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7276 (m) REVERT: A 413 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7320 (t0) REVERT: A 424 MET cc_start: 0.8370 (ttp) cc_final: 0.8169 (tmm) REVERT: C 149 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: C 333 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7803 (ttm110) REVERT: D 242 ARG cc_start: 0.8439 (ttm110) cc_final: 0.7930 (ttm-80) REVERT: D 321 MET cc_start: 0.8361 (mtp) cc_final: 0.8121 (mtt) REVERT: G 54 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7730 (mtt-85) REVERT: G 57 LYS cc_start: 0.8683 (mttt) cc_final: 0.8408 (mtmm) REVERT: B 476 ARG cc_start: 0.7667 (tmt170) cc_final: 0.7394 (tpp80) outliers start: 28 outliers final: 16 residues processed: 211 average time/residue: 1.2534 time to fit residues: 293.9459 Evaluate side-chains 213 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 291 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 202 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086959 restraints weight = 59288.499| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.85 r_work: 0.2990 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18615 Z= 0.124 Angle : 0.880 43.554 25416 Z= 0.360 Chirality : 0.046 0.451 3000 Planarity : 0.004 0.038 3078 Dihedral : 10.345 103.780 3259 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.06 % Allowed : 13.74 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.18), residues: 2135 helix: 2.98 (0.18), residues: 780 sheet: 0.36 (0.23), residues: 477 loop : 0.11 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.013 0.001 TYR B 139 PHE 0.015 0.001 PHE B 194 TRP 0.008 0.001 TRP D 196 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00278 (18562) covalent geometry : angle 0.54344 (25272) SS BOND : bond 0.01510 ( 15) SS BOND : angle 2.34026 ( 30) hydrogen bonds : bond 0.04420 ( 878) hydrogen bonds : angle 4.05196 ( 2769) link_ALPHA1-2 : bond 0.00144 ( 7) link_ALPHA1-2 : angle 1.94215 ( 21) link_ALPHA1-3 : bond 0.00678 ( 6) link_ALPHA1-3 : angle 1.43724 ( 18) link_ALPHA1-6 : bond 0.00759 ( 7) link_ALPHA1-6 : angle 1.77507 ( 21) link_BETA1-4 : bond 0.00352 ( 11) link_BETA1-4 : angle 2.01230 ( 33) link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 23.64337 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8331 (t0) cc_final: 0.8054 (m-30) REVERT: A 282 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: A 287 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7272 (m) REVERT: C 149 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: D 242 ARG cc_start: 0.8435 (ttm110) cc_final: 0.7906 (ttm-80) REVERT: F 49 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8164 (ttpm) REVERT: G 54 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7718 (mtt-85) REVERT: G 57 LYS cc_start: 0.8664 (mttt) cc_final: 0.8398 (mtmm) REVERT: B 476 ARG cc_start: 0.7656 (tmt170) cc_final: 0.7398 (tpp80) outliers start: 21 outliers final: 14 residues processed: 206 average time/residue: 1.3017 time to fit residues: 298.7166 Evaluate side-chains 209 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 164 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 174 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086634 restraints weight = 59553.368| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.86 r_work: 0.2986 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 18615 Z= 0.141 Angle : 0.887 43.656 25416 Z= 0.364 Chirality : 0.046 0.455 3000 Planarity : 0.004 0.038 3078 Dihedral : 10.240 101.757 3259 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.11 % Allowed : 13.64 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.18), residues: 2135 helix: 2.97 (0.18), residues: 784 sheet: 0.38 (0.23), residues: 478 loop : 0.13 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.012 0.001 TYR B 139 PHE 0.017 0.001 PHE B 194 TRP 0.010 0.001 TRP D 196 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00330 (18562) covalent geometry : angle 0.55826 (25272) SS BOND : bond 0.01200 ( 15) SS BOND : angle 2.54257 ( 30) hydrogen bonds : bond 0.04454 ( 878) hydrogen bonds : angle 4.02732 ( 2769) link_ALPHA1-2 : bond 0.00206 ( 7) link_ALPHA1-2 : angle 2.05375 ( 21) link_ALPHA1-3 : bond 0.00580 ( 6) link_ALPHA1-3 : angle 1.51411 ( 18) link_ALPHA1-6 : bond 0.00691 ( 7) link_ALPHA1-6 : angle 1.74735 ( 21) link_BETA1-4 : bond 0.00410 ( 11) link_BETA1-4 : angle 2.04049 ( 33) link_NAG-ASN : bond 0.00261 ( 7) link_NAG-ASN : angle 23.51332 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8304 (t0) cc_final: 0.8024 (m-30) REVERT: A 282 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: A 287 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7269 (m) REVERT: C 149 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: D 242 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7911 (ttm-80) REVERT: D 321 MET cc_start: 0.8346 (mtp) cc_final: 0.8107 (mtt) REVERT: F 49 LYS cc_start: 0.8507 (ttmm) cc_final: 0.7969 (ttpp) REVERT: G 54 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7666 (mtt-85) REVERT: G 57 LYS cc_start: 0.8668 (mttt) cc_final: 0.8404 (mtmm) REVERT: B 476 ARG cc_start: 0.7657 (tmt170) cc_final: 0.7397 (tpp80) outliers start: 22 outliers final: 16 residues processed: 208 average time/residue: 1.2659 time to fit residues: 293.6525 Evaluate side-chains 213 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain G residue 0 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 176 optimal weight: 0.1980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089303 restraints weight = 60216.233| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.86 r_work: 0.3025 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 18615 Z= 0.117 Angle : 0.877 43.667 25416 Z= 0.356 Chirality : 0.045 0.446 3000 Planarity : 0.004 0.038 3078 Dihedral : 9.907 101.056 3259 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.01 % Allowed : 13.69 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.18), residues: 2135 helix: 3.07 (0.18), residues: 784 sheet: 0.36 (0.23), residues: 476 loop : 0.16 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.012 0.001 TYR B 139 PHE 0.014 0.001 PHE B 194 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00268 (18562) covalent geometry : angle 0.53429 (25272) SS BOND : bond 0.01169 ( 15) SS BOND : angle 2.60551 ( 30) hydrogen bonds : bond 0.04217 ( 878) hydrogen bonds : angle 3.94550 ( 2769) link_ALPHA1-2 : bond 0.00127 ( 7) link_ALPHA1-2 : angle 1.88909 ( 21) link_ALPHA1-3 : bond 0.00652 ( 6) link_ALPHA1-3 : angle 1.42278 ( 18) link_ALPHA1-6 : bond 0.00699 ( 7) link_ALPHA1-6 : angle 1.74311 ( 21) link_BETA1-4 : bond 0.00341 ( 11) link_BETA1-4 : angle 1.90168 ( 33) link_NAG-ASN : bond 0.00358 ( 7) link_NAG-ASN : angle 23.75824 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14092.00 seconds wall clock time: 238 minutes 22.65 seconds (14302.65 seconds total)