Starting phenix.real_space_refine on Fri Aug 22 18:35:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yaa_39093/08_2025/8yaa_39093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yaa_39093/08_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_39093/08_2025/8yaa_39093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yaa_39093/08_2025/8yaa_39093.map" model { file = "/net/cci-nas-00/data/ceres_data/8yaa_39093/08_2025/8yaa_39093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yaa_39093/08_2025/8yaa_39093.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.01s 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: 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: 1.69, per 1000 atoms: 0.24 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: 0.73 Conformation dependent library (CDL) restraints added in 398.0 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.38 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: 1.19 Time building geometry restraints manager: 0.91 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.940 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.017 0.001 ARG A 583 TYR 0.017 0.002 TYR A 198 PHE 0.021 0.002 PHE A 354 TRP 0.012 0.001 TRP A 85 HIS 0.006 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 7110) covalent geometry : angle 0.87174 ( 9683) SS BOND : bond 0.00376 ( 4) SS BOND : angle 2.14671 ( 8) hydrogen bonds : bond 0.22725 ( 101) hydrogen bonds : angle 7.46065 ( 111) link_ALPHA1-3 : bond 0.01406 ( 1) link_ALPHA1-3 : angle 2.71644 ( 3) 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_NAG-ASN : bond 0.00583 ( 20) link_NAG-ASN : angle 5.50493 ( 60) *********************** 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 : 0.258 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: 0.0944 time to fit residues: 8.7311 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.124626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096445 restraints weight = 10572.841| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.65 r_work: 0.2930 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0900 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= 0.145 Angle : 0.861 16.747 9799 Z= 0.374 Chirality : 0.054 0.373 1239 Planarity : 0.005 0.054 1214 Dihedral : 19.765 116.456 1631 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.34 % Favored : 88.54 % Rotamer: Outliers : 0.92 % Allowed : 6.87 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.17 (0.27), residues: 838 helix: -3.91 (0.26), residues: 194 sheet: -3.76 (0.36), residues: 158 loop : -1.86 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.016 0.001 TYR A 198 PHE 0.013 0.002 PHE A 222 TRP 0.020 0.002 TRP A 85 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7110) covalent geometry : angle 0.76825 ( 9683) SS BOND : bond 0.00256 ( 4) SS BOND : angle 1.08382 ( 8) hydrogen bonds : bond 0.04273 ( 101) hydrogen bonds : angle 5.59387 ( 111) link_ALPHA1-3 : bond 0.01062 ( 1) link_ALPHA1-3 : angle 3.22511 ( 3) link_ALPHA1-6 : bond 0.00024 ( 1) link_ALPHA1-6 : angle 2.40557 ( 3) link_BETA1-4 : bond 0.01353 ( 14) link_BETA1-4 : angle 3.84773 ( 42) link_NAG-ASN : bond 0.00471 ( 20) link_NAG-ASN : angle 3.79929 ( 60) *********************** 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 57 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.200 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.0737 time to fit residues: 5.6217 Evaluate side-chains 50 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain A residue 525 ILE 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 14 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.124626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096385 restraints weight = 10559.841| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.60 r_work: 0.2924 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7150 Z= 0.137 Angle : 0.798 16.491 9799 Z= 0.347 Chirality : 0.051 0.383 1239 Planarity : 0.004 0.051 1214 Dihedral : 15.854 113.689 1631 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.71 % Favored : 91.17 % Rotamer: Outliers : 1.06 % Allowed : 10.83 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.16 (0.27), residues: 838 helix: -3.93 (0.25), residues: 196 sheet: -3.70 (0.36), residues: 164 loop : -1.82 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.014 0.001 TYR A 198 PHE 0.012 0.001 PHE A 222 TRP 0.007 0.001 TRP A 362 HIS 0.005 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7110) covalent geometry : angle 0.70997 ( 9683) SS BOND : bond 0.00491 ( 4) SS BOND : angle 1.36396 ( 8) hydrogen bonds : bond 0.03841 ( 101) hydrogen bonds : angle 4.92023 ( 111) link_ALPHA1-3 : bond 0.01606 ( 1) link_ALPHA1-3 : angle 2.21131 ( 3) link_ALPHA1-6 : bond 0.00230 ( 1) link_ALPHA1-6 : angle 2.13704 ( 3) link_BETA1-4 : bond 0.01355 ( 14) link_BETA1-4 : angle 3.71271 ( 42) link_NAG-ASN : bond 0.00464 ( 20) link_NAG-ASN : angle 3.50587 ( 60) *********************** 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 64 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6031 (p0) cc_final: 0.5700 (m-40) REVERT: A 273 GLN cc_start: 0.8363 (mt0) cc_final: 0.8110 (mt0) REVERT: A 611 ASP cc_start: 0.8271 (p0) cc_final: 0.7933 (p0) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.0788 time to fit residues: 6.6569 Evaluate side-chains 50 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 8 optimal weight: 6.9990 chunk 50 optimal weight: 0.0470 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 19 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.125973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097577 restraints weight = 10614.593| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.78 r_work: 0.2952 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7150 Z= 0.117 Angle : 0.757 16.643 9799 Z= 0.330 Chirality : 0.050 0.385 1239 Planarity : 0.004 0.050 1214 Dihedral : 14.565 113.524 1631 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.23 % Favored : 91.65 % Rotamer: Outliers : 1.72 % Allowed : 13.47 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.10 (0.27), residues: 838 helix: -3.87 (0.26), residues: 194 sheet: -3.86 (0.36), residues: 158 loop : -1.76 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.012 0.001 TYR A 198 PHE 0.010 0.001 PHE A 222 TRP 0.034 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7110) covalent geometry : angle 0.67028 ( 9683) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.46946 ( 8) hydrogen bonds : bond 0.03517 ( 101) hydrogen bonds : angle 4.69074 ( 111) link_ALPHA1-3 : bond 0.01317 ( 1) link_ALPHA1-3 : angle 2.92130 ( 3) link_ALPHA1-6 : bond 0.00183 ( 1) link_ALPHA1-6 : angle 1.83680 ( 3) link_BETA1-4 : bond 0.01345 ( 14) link_BETA1-4 : angle 3.67145 ( 42) link_NAG-ASN : bond 0.00478 ( 20) link_NAG-ASN : angle 3.28627 ( 60) *********************** 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: 13 poor density : 46 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6931 (t) REVERT: A 77 ASN cc_start: 0.6103 (p0) cc_final: 0.5633 (m-40) REVERT: A 611 ASP cc_start: 0.8226 (p0) cc_final: 0.7882 (p0) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.0713 time to fit residues: 5.6878 Evaluate side-chains 48 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.125069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096598 restraints weight = 10651.988| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.77 r_work: 0.2914 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1663 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= 0.129 Angle : 0.762 16.507 9799 Z= 0.331 Chirality : 0.051 0.374 1239 Planarity : 0.004 0.049 1214 Dihedral : 13.779 114.838 1631 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.43 % Favored : 90.45 % Rotamer: Outliers : 1.72 % Allowed : 16.25 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.10 (0.27), residues: 838 helix: -3.88 (0.26), residues: 195 sheet: -3.75 (0.36), residues: 169 loop : -1.71 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.013 0.001 TYR A 198 PHE 0.014 0.001 PHE A 222 TRP 0.025 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7110) covalent geometry : angle 0.67731 ( 9683) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.69318 ( 8) hydrogen bonds : bond 0.03417 ( 101) hydrogen bonds : angle 4.51851 ( 111) link_ALPHA1-3 : bond 0.01335 ( 1) link_ALPHA1-3 : angle 2.82068 ( 3) link_ALPHA1-6 : bond 0.00072 ( 1) link_ALPHA1-6 : angle 1.83016 ( 3) link_BETA1-4 : bond 0.01299 ( 14) link_BETA1-4 : angle 3.62466 ( 42) link_NAG-ASN : bond 0.00424 ( 20) link_NAG-ASN : angle 3.26932 ( 60) *********************** 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 60 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6898 (t) REVERT: A 77 ASN cc_start: 0.5997 (p0) cc_final: 0.5709 (m-40) REVERT: A 90 CYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6053 (p) REVERT: A 326 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 611 ASP cc_start: 0.8238 (p0) cc_final: 0.7876 (p0) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.0716 time to fit residues: 5.7930 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 : 0.194 ------------------------------------------------------------------------------- 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 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098909 restraints weight = 10626.820| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.68 r_work: 0.2968 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1884 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= 0.108 Angle : 0.721 16.492 9799 Z= 0.313 Chirality : 0.049 0.375 1239 Planarity : 0.004 0.049 1214 Dihedral : 12.924 113.199 1631 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.72 % Allowed : 16.91 % 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 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: -3.97 (0.27), residues: 838 helix: -3.82 (0.27), residues: 195 sheet: -3.69 (0.36), residues: 168 loop : -1.61 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.011 0.001 TYR A 198 PHE 0.009 0.001 PHE A 222 TRP 0.026 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7110) covalent geometry : angle 0.63717 ( 9683) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.12021 ( 8) hydrogen bonds : bond 0.03109 ( 101) hydrogen bonds : angle 4.40457 ( 111) link_ALPHA1-3 : bond 0.01330 ( 1) link_ALPHA1-3 : angle 2.68346 ( 3) link_ALPHA1-6 : bond 0.00162 ( 1) link_ALPHA1-6 : angle 1.61306 ( 3) link_BETA1-4 : bond 0.01307 ( 14) link_BETA1-4 : angle 3.63735 ( 42) link_NAG-ASN : bond 0.00449 ( 20) link_NAG-ASN : angle 3.08314 ( 60) *********************** 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 60 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6111 (p0) cc_final: 0.5694 (m-40) REVERT: A 90 CYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6129 (p) REVERT: A 611 ASP cc_start: 0.8209 (p0) cc_final: 0.7857 (p0) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.0683 time to fit residues: 5.5339 Evaluate side-chains 54 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 90 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 653 VAL 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 36 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.123834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095812 restraints weight = 10647.580| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.66 r_work: 0.2921 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7150 Z= 0.153 Angle : 0.782 16.569 9799 Z= 0.340 Chirality : 0.051 0.372 1239 Planarity : 0.004 0.050 1214 Dihedral : 12.394 112.371 1631 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 1.98 % Allowed : 15.98 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.00 (0.27), residues: 838 helix: -3.83 (0.26), residues: 194 sheet: -3.74 (0.36), residues: 169 loop : -1.61 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 619 TYR 0.016 0.002 TYR A 198 PHE 0.015 0.001 PHE A 222 TRP 0.015 0.001 TRP A 85 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7110) covalent geometry : angle 0.69802 ( 9683) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.57666 ( 8) hydrogen bonds : bond 0.03542 ( 101) hydrogen bonds : angle 4.59544 ( 111) link_ALPHA1-3 : bond 0.01316 ( 1) link_ALPHA1-3 : angle 3.08585 ( 3) link_ALPHA1-6 : bond 0.00080 ( 1) link_ALPHA1-6 : angle 1.89008 ( 3) link_BETA1-4 : bond 0.01288 ( 14) link_BETA1-4 : angle 3.66369 ( 42) link_NAG-ASN : bond 0.00404 ( 20) link_NAG-ASN : angle 3.28734 ( 60) *********************** 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: 15 poor density : 45 time to evaluate : 0.262 Fit side-chains REVERT: A 47 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6799 (t) REVERT: A 77 ASN cc_start: 0.5938 (p0) cc_final: 0.5550 (m-40) REVERT: A 90 CYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6131 (p) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.0730 time to fit residues: 5.8517 Evaluate side-chains 52 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 525 ILE Chi-restraints excluded: chain A residue 641 SER 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 67 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.126957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098924 restraints weight = 10648.420| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.92 r_work: 0.2975 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2086 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= 0.104 Angle : 0.712 16.425 9799 Z= 0.310 Chirality : 0.048 0.373 1239 Planarity : 0.004 0.052 1214 Dihedral : 11.543 111.105 1631 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.45 % Allowed : 16.78 % 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 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: -3.96 (0.27), residues: 838 helix: -3.81 (0.26), residues: 201 sheet: -3.70 (0.36), residues: 168 loop : -1.55 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.010 0.001 TYR A 198 PHE 0.009 0.001 PHE A 222 TRP 0.030 0.001 TRP A 85 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7110) covalent geometry : angle 0.62729 ( 9683) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.07194 ( 8) hydrogen bonds : bond 0.03005 ( 101) hydrogen bonds : angle 4.32145 ( 111) link_ALPHA1-3 : bond 0.01246 ( 1) link_ALPHA1-3 : angle 2.49395 ( 3) link_ALPHA1-6 : bond 0.00239 ( 1) link_ALPHA1-6 : angle 1.46237 ( 3) link_BETA1-4 : bond 0.01309 ( 14) link_BETA1-4 : angle 3.71689 ( 42) link_NAG-ASN : bond 0.00451 ( 20) link_NAG-ASN : angle 3.00931 ( 60) *********************** 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 60 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6012 (p0) cc_final: 0.5638 (m-40) REVERT: A 90 CYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6078 (p) REVERT: A 326 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 611 ASP cc_start: 0.8201 (p0) cc_final: 0.7850 (p0) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.0821 time to fit residues: 6.4610 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 : 0.212 ------------------------------------------------------------------------------- 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 90 CYS Chi-restraints excluded: chain A residue 151 ILE 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 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.126697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098797 restraints weight = 10695.051| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.88 r_work: 0.2975 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2168 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 16.474 9799 Z= 0.311 Chirality : 0.048 0.370 1239 Planarity : 0.004 0.051 1214 Dihedral : 11.091 108.250 1631 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 1.59 % Allowed : 16.78 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.92 (0.27), residues: 838 helix: -3.80 (0.26), residues: 200 sheet: -3.59 (0.38), residues: 159 loop : -1.61 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.012 0.001 TYR A 198 PHE 0.012 0.001 PHE A 222 TRP 0.021 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7110) covalent geometry : angle 0.62826 ( 9683) SS BOND : bond 0.00243 ( 4) SS BOND : angle 1.13733 ( 8) hydrogen bonds : bond 0.03037 ( 101) hydrogen bonds : angle 4.35441 ( 111) link_ALPHA1-3 : bond 0.01220 ( 1) link_ALPHA1-3 : angle 2.75901 ( 3) link_ALPHA1-6 : bond 0.00171 ( 1) link_ALPHA1-6 : angle 1.59710 ( 3) link_BETA1-4 : bond 0.01290 ( 14) link_BETA1-4 : angle 3.63937 ( 42) link_NAG-ASN : bond 0.00415 ( 20) link_NAG-ASN : angle 3.05434 ( 60) *********************** 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: 12 poor density : 46 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.5925 (p0) cc_final: 0.5600 (m-40) REVERT: A 90 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.5992 (p) REVERT: A 326 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8257 (mm) REVERT: A 611 ASP cc_start: 0.8182 (p0) cc_final: 0.7825 (p0) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.0671 time to fit residues: 5.4168 Evaluate side-chains 56 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 90 CYS Chi-restraints excluded: chain A residue 151 ILE 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 653 VAL 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 55 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097924 restraints weight = 10590.123| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.86 r_work: 0.2958 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2158 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= 0.127 Angle : 0.719 16.508 9799 Z= 0.316 Chirality : 0.049 0.373 1239 Planarity : 0.004 0.051 1214 Dihedral : 10.798 108.394 1631 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.72 % Allowed : 16.91 % 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 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: -3.93 (0.27), residues: 838 helix: -3.80 (0.26), residues: 196 sheet: -3.67 (0.36), residues: 178 loop : -1.49 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.013 0.001 TYR A 198 PHE 0.012 0.001 PHE A 222 TRP 0.020 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7110) covalent geometry : angle 0.63471 ( 9683) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.27586 ( 8) hydrogen bonds : bond 0.03153 ( 101) hydrogen bonds : angle 4.33535 ( 111) link_ALPHA1-3 : bond 0.01197 ( 1) link_ALPHA1-3 : angle 2.80185 ( 3) link_ALPHA1-6 : bond 0.00139 ( 1) link_ALPHA1-6 : angle 1.62023 ( 3) link_BETA1-4 : bond 0.01290 ( 14) link_BETA1-4 : angle 3.62274 ( 42) link_NAG-ASN : bond 0.00410 ( 20) link_NAG-ASN : angle 3.08661 ( 60) ********************** 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 57 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6082 (p0) cc_final: 0.5745 (m-40) REVERT: A 90 CYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6285 (p) REVERT: A 326 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 334 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: A 336 MET cc_start: 0.8668 (tpp) cc_final: 0.8110 (tpt) REVERT: A 611 ASP cc_start: 0.8337 (p0) cc_final: 0.7971 (p0) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.0604 time to fit residues: 4.8422 Evaluate side-chains 56 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 90 CYS Chi-restraints excluded: chain A residue 151 ILE 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 653 VAL 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 67 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099677 restraints weight = 10514.170| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.67 r_work: 0.2986 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7150 Z= 0.102 Angle : 0.681 16.377 9799 Z= 0.299 Chirality : 0.047 0.369 1239 Planarity : 0.004 0.051 1214 Dihedral : 10.390 106.275 1631 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.72 % Allowed : 16.78 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.92 (0.28), residues: 838 helix: -3.79 (0.26), residues: 202 sheet: -3.61 (0.36), residues: 174 loop : -1.50 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.009 0.001 TYR A 198 PHE 0.010 0.001 PHE A 222 TRP 0.021 0.001 TRP A 85 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7110) covalent geometry : angle 0.59724 ( 9683) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.94842 ( 8) hydrogen bonds : bond 0.02867 ( 101) hydrogen bonds : angle 4.22225 ( 111) link_ALPHA1-3 : bond 0.01105 ( 1) link_ALPHA1-3 : angle 2.44912 ( 3) link_ALPHA1-6 : bond 0.00305 ( 1) link_ALPHA1-6 : angle 1.48304 ( 3) link_BETA1-4 : bond 0.01274 ( 14) link_BETA1-4 : angle 3.55199 ( 42) link_NAG-ASN : bond 0.00420 ( 20) link_NAG-ASN : angle 2.97949 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.21 seconds wall clock time: 24 minutes 30.17 seconds (1470.17 seconds total)