Starting phenix.real_space_refine on Sat May 10 20:59:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yaa_39093/05_2025/8yaa_39093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yaa_39093/05_2025/8yaa_39093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yaa_39093/05_2025/8yaa_39093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yaa_39093/05_2025/8yaa_39093.map" model { file = "/net/cci-nas-00/data/ceres_data/8yaa_39093/05_2025/8yaa_39093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yaa_39093/05_2025/8yaa_39093.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 4372 2.51 5 N 1132 2.21 5 O 1462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6985 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1347 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "A" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5054 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 42, 'TRANS': 611} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 92 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" 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: "L" 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: "M" 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: "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: "O" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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 Time building chain proxies: 4.48, per 1000 atoms: 0.64 Number of scatterers: 6985 At special positions: 0 Unit cell: (111.35, 88.4, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 1462 8.00 N 1132 7.00 C 4372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 403 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS A 695 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 701 " - " ASN A 633 " " NAG A 702 " - " ASN A 393 " " NAG A 703 " - " ASN A 249 " " NAG A 704 " - " ASN A 63 " " NAG A 705 " - " ASN A 119 " " NAG A 706 " - " ASN A 99 " " NAG C 301 " - " ASN C 114 " " NAG C 302 " - " ASN C 103 " " NAG D 1 " - " ASN A 410 " " NAG E 1 " - " ASN C 183 " " NAG F 1 " - " ASN C 149 " " NAG G 1 " - " ASN A 212 " " NAG H 1 " - " ASN A 179 " " NAG I 1 " - " ASN A 580 " " NAG J 1 " - " ASN A 487 " " NAG K 1 " - " ASN A 323 " " NAG L 1 " - " ASN A 263 " " NAG M 1 " - " ASN A 500 " " NAG N 1 " - " ASN A 380 " " NAG O 1 " - " ASN A 284 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 891.6 milliseconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 23.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.509A pdb=" N ASP C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.779A pdb=" N LEU C 88 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.609A pdb=" N LEU C 115 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.854A pdb=" N LEU C 136 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 139 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.665A pdb=" N SER A 72 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.774A pdb=" N THR A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 141 removed outlier: 4.043A pdb=" N PHE A 141 " --> pdb=" O TRP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.544A pdb=" N LEU A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.584A pdb=" N PHE A 210 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.545A pdb=" N LEU A 237 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.676A pdb=" N MET A 285 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.502A pdb=" N LEU A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 309 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.990A pdb=" N PHE A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.838A pdb=" N ALA A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 380 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 4.140A pdb=" N PHE A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.776A pdb=" N ILE A 525 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.527A pdb=" N ARG A 619 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.730A pdb=" N PHE A 642 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.589A pdb=" N ALA A 675 " --> pdb=" O PRO A 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 39 through 40 removed outlier: 5.702A pdb=" N GLY C 82 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR C 107 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 104 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER C 129 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY C 106 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 64 removed outlier: 7.036A pdb=" N THR C 63 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR C 71 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLU C 98 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 73 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU C 97 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 121 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.980A pdb=" N ALA A 89 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N PHE A 122 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 96 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASP A 124 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 98 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 147 " --> pdb=" O HIS A 172 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 195 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 219 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 243 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 267 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 291 " --> pdb=" O HIS A 316 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 315 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 339 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 363 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 387 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 411 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 459 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 483 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 507 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 555 " --> pdb=" O ASN A 580 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N MET A 579 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 603 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 627 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 4.246A pdb=" N GLY A 107 " --> pdb=" O ARG A 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 155 through 156 removed outlier: 4.184A pdb=" N GLY A 156 " --> pdb=" O LYS A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 228 removed outlier: 5.893A pdb=" N GLY A 228 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 250 " --> pdb=" O GLN A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.626A pdb=" N GLY A 324 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 346 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER A 371 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLY A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 370 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 395 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLY A 372 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 394 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU A 419 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY A 396 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 418 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 443 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY A 420 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP A 445 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE A 442 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS A 467 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY A 444 " --> pdb=" O HIS A 467 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 466 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR A 491 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY A 468 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 493 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 490 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 515 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A 492 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 514 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 539 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY A 516 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 538 " --> pdb=" O ARG A 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 611 through 612 removed outlier: 5.650A pdb=" N GLY A 612 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN A 637 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 634 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN A 659 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY A 636 " --> pdb=" O GLN A 659 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 681 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 683 " --> pdb=" O GLY A 660 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 111 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: 1.98 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2223 1.34 - 1.46: 1381 1.46 - 1.58: 3477 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 7110 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.410 1.472 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.48e+00 bond pdb=" N PHE A 222 " pdb=" CA PHE A 222 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.34e-02 5.57e+03 8.25e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.11e+00 ... (remaining 7105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9325 2.09 - 4.19: 307 4.19 - 6.28: 44 6.28 - 8.38: 6 8.38 - 10.47: 1 Bond angle restraints: 9683 Sorted by residual: angle pdb=" N GLY C 82 " pdb=" CA GLY C 82 " pdb=" C GLY C 82 " ideal model delta sigma weight residual 110.20 117.05 -6.85 1.32e+00 5.74e-01 2.70e+01 angle pdb=" C GLN A 588 " pdb=" N THR A 589 " pdb=" CA THR A 589 " ideal model delta sigma weight residual 121.31 128.49 -7.18 1.49e+00 4.50e-01 2.32e+01 angle pdb=" N THR A 589 " pdb=" CA THR A 589 " pdb=" C THR A 589 " ideal model delta sigma weight residual 110.35 116.62 -6.27 1.40e+00 5.10e-01 2.00e+01 angle pdb=" C ASN A 224 " pdb=" N SER A 225 " pdb=" CA SER A 225 " ideal model delta sigma weight residual 122.24 116.59 5.65 1.46e+00 4.69e-01 1.50e+01 angle pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " pdb=" CG PHE A 222 " ideal model delta sigma weight residual 113.80 117.62 -3.82 1.00e+00 1.00e+00 1.46e+01 ... (remaining 9678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.29: 4403 25.29 - 50.59: 255 50.59 - 75.88: 44 75.88 - 101.18: 26 101.18 - 126.47: 55 Dihedral angle restraints: 4783 sinusoidal: 2359 harmonic: 2424 Sorted by residual: dihedral pdb=" CB CYS A 82 " pdb=" SG CYS A 82 " pdb=" SG CYS A 90 " pdb=" CB CYS A 90 " ideal model delta sinusoidal sigma weight residual 93.00 152.43 -59.43 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CA SER A 150 " pdb=" C SER A 150 " pdb=" N ILE A 151 " pdb=" CA ILE A 151 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN A 632 " pdb=" C ASN A 632 " pdb=" N ASN A 633 " pdb=" CA ASN A 633 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 4780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1129 0.092 - 0.184: 95 0.184 - 0.276: 7 0.276 - 0.368: 4 0.368 - 0.459: 4 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 8.79e+01 chirality pdb=" C1 MAN D 5 " pdb=" O6 BMA D 3 " pdb=" C2 MAN D 5 " pdb=" O5 MAN D 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.53e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 1236 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 633 " 0.036 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" CG ASN A 633 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 633 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 633 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 249 " 0.030 2.00e-02 2.50e+03 2.76e-02 9.53e+00 pdb=" CG ASN A 249 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 249 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 249 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 500 " -0.005 2.00e-02 2.50e+03 2.44e-02 7.46e+00 pdb=" CG ASN A 500 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 500 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 500 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.024 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 211 2.69 - 3.24: 6887 3.24 - 3.79: 10260 3.79 - 4.35: 14095 4.35 - 4.90: 22922 Nonbonded interactions: 54375 Sorted by model distance: nonbonded pdb=" O PHE C 194 " pdb=" OG1 THR C 197 " model vdw 2.131 3.040 nonbonded pdb=" O3 NAG E 1 " pdb=" O5 NAG E 2 " model vdw 2.176 3.040 nonbonded pdb=" O LYS A 310 " pdb=" OG SER A 335 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU A 242 " pdb=" OG SER B 4 " model vdw 2.225 3.040 nonbonded pdb=" O ARG A 129 " pdb=" NE2 GLN A 153 " model vdw 2.239 3.120 ... (remaining 54370 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=1.00 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: 0.650 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.580 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.006 0.079 7150 Z= 0.277 Angle : 1.008 18.280 9799 Z= 0.470 Chirality : 0.061 0.459 1239 Planarity : 0.005 0.059 1214 Dihedral : 21.923 126.469 3201 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.13 % Allowed : 0.53 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.27), residues: 838 helix: -3.94 (0.26), residues: 179 sheet: -3.56 (0.40), residues: 142 loop : -2.00 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 85 HIS 0.006 0.001 HIS A 294 PHE 0.021 0.002 PHE A 354 TYR 0.017 0.002 TYR A 198 ARG 0.017 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 20) link_NAG-ASN : angle 5.50493 ( 60) link_ALPHA1-6 : bond 0.01598 ( 1) link_ALPHA1-6 : angle 4.75446 ( 3) link_BETA1-4 : bond 0.01491 ( 14) link_BETA1-4 : angle 3.95117 ( 42) link_ALPHA1-3 : bond 0.01406 ( 1) link_ALPHA1-3 : angle 2.71644 ( 3) hydrogen bonds : bond 0.22725 ( 101) hydrogen bonds : angle 7.46065 ( 111) SS BOND : bond 0.00376 ( 4) SS BOND : angle 2.14671 ( 8) covalent geometry : bond 0.00567 ( 7110) covalent geometry : angle 0.87174 ( 9683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.851 Fit side-chains REVERT: A 475 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7285 (tp30) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.2437 time to fit residues: 23.0002 Evaluate side-chains 48 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098192 restraints weight = 10369.924| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.65 r_work: 0.2965 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7150 Z= 0.123 Angle : 0.839 16.771 9799 Z= 0.362 Chirality : 0.053 0.379 1239 Planarity : 0.005 0.054 1214 Dihedral : 19.481 116.067 1631 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.79 % Favored : 90.10 % Rotamer: Outliers : 0.79 % Allowed : 6.34 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.27), residues: 838 helix: -3.91 (0.26), residues: 195 sheet: -3.61 (0.38), residues: 157 loop : -1.86 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 85 HIS 0.005 0.001 HIS A 294 PHE 0.012 0.001 PHE A 81 TYR 0.015 0.001 TYR A 198 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 20) link_NAG-ASN : angle 3.71601 ( 60) link_ALPHA1-6 : bond 0.00449 ( 1) link_ALPHA1-6 : angle 2.42127 ( 3) link_BETA1-4 : bond 0.01320 ( 14) link_BETA1-4 : angle 3.87777 ( 42) link_ALPHA1-3 : bond 0.01054 ( 1) link_ALPHA1-3 : angle 3.11717 ( 3) hydrogen bonds : bond 0.03943 ( 101) hydrogen bonds : angle 5.44413 ( 111) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.94294 ( 8) covalent geometry : bond 0.00263 ( 7110) covalent geometry : angle 0.74593 ( 9683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.805 Fit side-chains REVERT: A 611 ASP cc_start: 0.8241 (p0) cc_final: 0.7912 (p0) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2086 time to fit residues: 17.0340 Evaluate side-chains 49 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095731 restraints weight = 10598.790| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.59 r_work: 0.2912 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7150 Z= 0.151 Angle : 0.815 16.480 9799 Z= 0.355 Chirality : 0.052 0.380 1239 Planarity : 0.005 0.050 1214 Dihedral : 15.936 112.911 1631 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.38 % Favored : 89.50 % Rotamer: Outliers : 1.06 % Allowed : 10.44 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.27), residues: 838 helix: -3.91 (0.26), residues: 194 sheet: -3.70 (0.36), residues: 164 loop : -1.84 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.005 0.001 HIS A 172 PHE 0.014 0.001 PHE A 222 TYR 0.016 0.001 TYR A 198 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 20) link_NAG-ASN : angle 3.53436 ( 60) link_ALPHA1-6 : bond 0.00138 ( 1) link_ALPHA1-6 : angle 2.18810 ( 3) link_BETA1-4 : bond 0.01352 ( 14) link_BETA1-4 : angle 3.69002 ( 42) link_ALPHA1-3 : bond 0.01581 ( 1) link_ALPHA1-3 : angle 2.42477 ( 3) hydrogen bonds : bond 0.04033 ( 101) hydrogen bonds : angle 4.94470 ( 111) SS BOND : bond 0.00348 ( 4) SS BOND : angle 1.55964 ( 8) covalent geometry : bond 0.00351 ( 7110) covalent geometry : angle 0.72870 ( 9683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6004 (p0) cc_final: 0.5665 (m-40) REVERT: A 611 ASP cc_start: 0.8237 (p0) cc_final: 0.7902 (p0) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1901 time to fit residues: 15.9657 Evaluate side-chains 51 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 525 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 3 optimal weight: 0.0770 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095655 restraints weight = 10673.656| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.75 r_work: 0.2919 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7150 Z= 0.153 Angle : 0.800 16.503 9799 Z= 0.350 Chirality : 0.052 0.382 1239 Planarity : 0.004 0.049 1214 Dihedral : 14.822 112.102 1631 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.02 % Favored : 89.86 % Rotamer: Outliers : 1.85 % Allowed : 13.74 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.27), residues: 838 helix: -3.92 (0.26), residues: 195 sheet: -3.82 (0.35), residues: 169 loop : -1.79 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 85 HIS 0.005 0.001 HIS A 172 PHE 0.013 0.001 PHE A 222 TYR 0.014 0.002 TYR A 198 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 20) link_NAG-ASN : angle 3.41545 ( 60) link_ALPHA1-6 : bond 0.00000 ( 1) link_ALPHA1-6 : angle 2.02127 ( 3) link_BETA1-4 : bond 0.01321 ( 14) link_BETA1-4 : angle 3.66900 ( 42) link_ALPHA1-3 : bond 0.01320 ( 1) link_ALPHA1-3 : angle 3.08370 ( 3) hydrogen bonds : bond 0.03821 ( 101) hydrogen bonds : angle 4.77780 ( 111) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.89481 ( 8) covalent geometry : bond 0.00357 ( 7110) covalent geometry : angle 0.71399 ( 9683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.852 Fit side-chains REVERT: A 47 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6972 (t) REVERT: A 77 ASN cc_start: 0.6193 (p0) cc_final: 0.5668 (m-40) REVERT: A 90 CYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6145 (p) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.1994 time to fit residues: 16.0100 Evaluate side-chains 50 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091481 restraints weight = 10686.512| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.85 r_work: 0.2850 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7150 Z= 0.282 Angle : 0.955 16.589 9799 Z= 0.423 Chirality : 0.058 0.379 1239 Planarity : 0.005 0.049 1214 Dihedral : 14.711 112.206 1631 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.01 % Favored : 86.87 % Rotamer: Outliers : 2.25 % Allowed : 15.98 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.26), residues: 838 helix: -3.96 (0.26), residues: 186 sheet: -3.37 (0.41), residues: 148 loop : -2.09 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 85 HIS 0.010 0.002 HIS A 172 PHE 0.016 0.002 PHE A 270 TYR 0.019 0.002 TYR A 198 ARG 0.004 0.001 ARG A 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 20) link_NAG-ASN : angle 3.81224 ( 60) link_ALPHA1-6 : bond 0.00495 ( 1) link_ALPHA1-6 : angle 2.39575 ( 3) link_BETA1-4 : bond 0.01342 ( 14) link_BETA1-4 : angle 3.79991 ( 42) link_ALPHA1-3 : bond 0.01392 ( 1) link_ALPHA1-3 : angle 3.40878 ( 3) hydrogen bonds : bond 0.04573 ( 101) hydrogen bonds : angle 5.19529 ( 111) SS BOND : bond 0.00440 ( 4) SS BOND : angle 2.47167 ( 8) covalent geometry : bond 0.00688 ( 7110) covalent geometry : angle 0.87206 ( 9683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.830 Fit side-chains REVERT: A 47 THR cc_start: 0.7228 (OUTLIER) cc_final: 0.7019 (t) REVERT: A 90 CYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6336 (p) REVERT: A 326 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8362 (mm) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 0.1981 time to fit residues: 16.1205 Evaluate side-chains 53 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 592 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 81 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095636 restraints weight = 10603.009| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.88 r_work: 0.2894 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7150 Z= 0.125 Angle : 0.770 16.607 9799 Z= 0.337 Chirality : 0.051 0.380 1239 Planarity : 0.004 0.051 1214 Dihedral : 13.719 113.591 1631 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.28 % Favored : 92.60 % Rotamer: Outliers : 1.72 % Allowed : 16.51 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.27), residues: 838 helix: -3.87 (0.27), residues: 188 sheet: -3.79 (0.36), residues: 169 loop : -1.74 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 PHE 0.011 0.001 PHE A 222 TYR 0.011 0.001 TYR A 198 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 20) link_NAG-ASN : angle 3.28387 ( 60) link_ALPHA1-6 : bond 0.00099 ( 1) link_ALPHA1-6 : angle 1.62306 ( 3) link_BETA1-4 : bond 0.01310 ( 14) link_BETA1-4 : angle 3.73045 ( 42) link_ALPHA1-3 : bond 0.01401 ( 1) link_ALPHA1-3 : angle 2.54786 ( 3) hydrogen bonds : bond 0.03399 ( 101) hydrogen bonds : angle 4.67565 ( 111) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.37355 ( 8) covalent geometry : bond 0.00275 ( 7110) covalent geometry : angle 0.68420 ( 9683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 47 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6943 (t) REVERT: A 77 ASN cc_start: 0.6081 (p0) cc_final: 0.5816 (m-40) REVERT: A 85 TRP cc_start: 0.8101 (m-10) cc_final: 0.7725 (m100) REVERT: A 90 CYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6259 (p) REVERT: A 334 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: A 513 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7658 (mtt-85) outliers start: 13 outliers final: 7 residues processed: 60 average time/residue: 0.2296 time to fit residues: 18.7463 Evaluate side-chains 55 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.093457 restraints weight = 10622.072| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.70 r_work: 0.2876 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7150 Z= 0.190 Angle : 0.842 16.617 9799 Z= 0.369 Chirality : 0.054 0.376 1239 Planarity : 0.005 0.050 1214 Dihedral : 13.360 112.259 1631 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 2.11 % Allowed : 16.51 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.26), residues: 838 helix: -3.89 (0.26), residues: 193 sheet: -3.78 (0.35), residues: 174 loop : -1.81 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 85 HIS 0.005 0.001 HIS A 294 PHE 0.017 0.001 PHE A 222 TYR 0.016 0.002 TYR A 198 ARG 0.002 0.000 ARG A 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 20) link_NAG-ASN : angle 3.50279 ( 60) link_ALPHA1-6 : bond 0.00273 ( 1) link_ALPHA1-6 : angle 1.99585 ( 3) link_BETA1-4 : bond 0.01296 ( 14) link_BETA1-4 : angle 3.73531 ( 42) link_ALPHA1-3 : bond 0.01415 ( 1) link_ALPHA1-3 : angle 3.09032 ( 3) hydrogen bonds : bond 0.03878 ( 101) hydrogen bonds : angle 4.83981 ( 111) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.75077 ( 8) covalent geometry : bond 0.00455 ( 7110) covalent geometry : angle 0.75811 ( 9683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.813 Fit side-chains REVERT: A 47 THR cc_start: 0.7164 (OUTLIER) cc_final: 0.6908 (t) REVERT: A 85 TRP cc_start: 0.8107 (m-10) cc_final: 0.7838 (m100) REVERT: A 90 CYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6364 (p) REVERT: A 326 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 334 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: A 629 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8740 (mp) outliers start: 16 outliers final: 10 residues processed: 58 average time/residue: 0.1981 time to fit residues: 15.9823 Evaluate side-chains 58 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095764 restraints weight = 10589.488| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.87 r_work: 0.2875 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7150 Z= 0.126 Angle : 0.768 16.604 9799 Z= 0.335 Chirality : 0.051 0.378 1239 Planarity : 0.004 0.051 1214 Dihedral : 12.650 111.988 1631 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.40 % Favored : 92.48 % Rotamer: Outliers : 2.38 % Allowed : 16.64 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.27), residues: 838 helix: -3.83 (0.26), residues: 193 sheet: -3.78 (0.37), residues: 164 loop : -1.71 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 PHE 0.012 0.001 PHE A 222 TYR 0.012 0.001 TYR A 198 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 20) link_NAG-ASN : angle 3.25035 ( 60) link_ALPHA1-6 : bond 0.00119 ( 1) link_ALPHA1-6 : angle 1.65236 ( 3) link_BETA1-4 : bond 0.01323 ( 14) link_BETA1-4 : angle 3.71007 ( 42) link_ALPHA1-3 : bond 0.01381 ( 1) link_ALPHA1-3 : angle 2.56405 ( 3) hydrogen bonds : bond 0.03367 ( 101) hydrogen bonds : angle 4.56407 ( 111) SS BOND : bond 0.00245 ( 4) SS BOND : angle 1.27275 ( 8) covalent geometry : bond 0.00283 ( 7110) covalent geometry : angle 0.68343 ( 9683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 47 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6885 (t) REVERT: A 77 ASN cc_start: 0.6201 (p0) cc_final: 0.5900 (m-40) REVERT: A 85 TRP cc_start: 0.8090 (m-10) cc_final: 0.7850 (m100) REVERT: A 90 CYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6225 (p) REVERT: A 326 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8357 (mm) REVERT: A 334 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7877 (pm20) outliers start: 18 outliers final: 10 residues processed: 66 average time/residue: 0.1830 time to fit residues: 16.7779 Evaluate side-chains 57 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097081 restraints weight = 10646.456| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.95 r_work: 0.2950 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7150 Z= 0.110 Angle : 0.739 16.487 9799 Z= 0.321 Chirality : 0.049 0.374 1239 Planarity : 0.004 0.053 1214 Dihedral : 11.509 108.598 1631 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.71 % Favored : 91.17 % Rotamer: Outliers : 1.32 % Allowed : 17.97 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.27), residues: 838 helix: -3.79 (0.27), residues: 200 sheet: -3.63 (0.37), residues: 163 loop : -1.64 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 85 HIS 0.003 0.001 HIS A 294 PHE 0.010 0.001 PHE A 222 TYR 0.011 0.001 TYR A 198 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 20) link_NAG-ASN : angle 3.15112 ( 60) link_ALPHA1-6 : bond 0.00255 ( 1) link_ALPHA1-6 : angle 1.54646 ( 3) link_BETA1-4 : bond 0.01311 ( 14) link_BETA1-4 : angle 3.68024 ( 42) link_ALPHA1-3 : bond 0.01326 ( 1) link_ALPHA1-3 : angle 2.49235 ( 3) hydrogen bonds : bond 0.03041 ( 101) hydrogen bonds : angle 4.44578 ( 111) SS BOND : bond 0.00227 ( 4) SS BOND : angle 1.00531 ( 8) covalent geometry : bond 0.00240 ( 7110) covalent geometry : angle 0.65434 ( 9683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6224 (p0) cc_final: 0.5982 (m-40) REVERT: A 326 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8319 (mm) REVERT: A 611 ASP cc_start: 0.8254 (p0) cc_final: 0.7881 (p0) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.2046 time to fit residues: 16.4164 Evaluate side-chains 54 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097499 restraints weight = 10763.859| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.96 r_work: 0.2930 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7150 Z= 0.117 Angle : 0.734 16.456 9799 Z= 0.322 Chirality : 0.049 0.372 1239 Planarity : 0.004 0.053 1214 Dihedral : 11.077 107.455 1631 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.92 % Favored : 92.96 % Rotamer: Outliers : 1.72 % Allowed : 17.70 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.27), residues: 838 helix: -3.80 (0.26), residues: 200 sheet: -3.58 (0.38), residues: 159 loop : -1.62 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP A 85 HIS 0.004 0.001 HIS A 294 PHE 0.012 0.001 PHE A 222 TYR 0.012 0.001 TYR A 198 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 20) link_NAG-ASN : angle 3.10853 ( 60) link_ALPHA1-6 : bond 0.00232 ( 1) link_ALPHA1-6 : angle 1.60406 ( 3) link_BETA1-4 : bond 0.01285 ( 14) link_BETA1-4 : angle 3.67718 ( 42) link_ALPHA1-3 : bond 0.01256 ( 1) link_ALPHA1-3 : angle 2.68265 ( 3) hydrogen bonds : bond 0.03086 ( 101) hydrogen bonds : angle 4.13383 ( 111) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.11559 ( 8) covalent geometry : bond 0.00259 ( 7110) covalent geometry : angle 0.65046 ( 9683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6131 (p0) cc_final: 0.5865 (m-40) REVERT: A 90 CYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6274 (p) REVERT: A 326 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 475 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7777 (tp30) REVERT: A 611 ASP cc_start: 0.8235 (p0) cc_final: 0.7846 (p0) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.1899 time to fit residues: 15.5265 Evaluate side-chains 56 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098276 restraints weight = 10628.431| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.98 r_work: 0.2957 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7150 Z= 0.111 Angle : 0.713 16.468 9799 Z= 0.313 Chirality : 0.048 0.372 1239 Planarity : 0.004 0.053 1214 Dihedral : 10.653 107.233 1631 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.72 % Allowed : 17.70 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.27), residues: 838 helix: -3.79 (0.27), residues: 200 sheet: -3.59 (0.38), residues: 159 loop : -1.57 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 85 HIS 0.004 0.001 HIS A 294 PHE 0.010 0.001 PHE A 222 TYR 0.011 0.001 TYR A 198 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 20) link_NAG-ASN : angle 3.03916 ( 60) link_ALPHA1-6 : bond 0.00257 ( 1) link_ALPHA1-6 : angle 1.50387 ( 3) link_BETA1-4 : bond 0.01306 ( 14) link_BETA1-4 : angle 3.60808 ( 42) link_ALPHA1-3 : bond 0.01268 ( 1) link_ALPHA1-3 : angle 2.59695 ( 3) hydrogen bonds : bond 0.02967 ( 101) hydrogen bonds : angle 4.08873 ( 111) SS BOND : bond 0.00358 ( 4) SS BOND : angle 1.27089 ( 8) covalent geometry : bond 0.00242 ( 7110) covalent geometry : angle 0.62940 ( 9683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3122.61 seconds wall clock time: 55 minutes 7.47 seconds (3307.47 seconds total)