Starting phenix.real_space_refine on Tue Jan 14 15:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yaa_39093/01_2025/8yaa_39093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yaa_39093/01_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_39093/01_2025/8yaa_39093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yaa_39093/01_2025/8yaa_39093.map" model { file = "/net/cci-nas-00/data/ceres_data/8yaa_39093/01_2025/8yaa_39093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yaa_39093/01_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-5571/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: 4.60, per 1000 atoms: 0.66 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: 2.16 Conformation dependent library (CDL) restraints added in 973.6 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: 0.90 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: 2.16 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: 0.670 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.120 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- 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 7110 Z= 0.345 Angle : 0.872 10.469 9683 Z= 0.440 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 *********************** 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 : 0.710 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: 0.2286 time to fit residues: 21.4839 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 : 0.794 ------------------------------------------------------------------------------- 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: 0.4980 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 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: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.126932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098754 restraints weight = 10361.223| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.67 r_work: 0.2973 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7110 Z= 0.173 Angle : 0.738 9.607 9683 Z= 0.337 Chirality : 0.053 0.379 1239 Planarity : 0.005 0.053 1214 Dihedral : 19.725 116.770 1631 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.95 % Favored : 90.93 % Rotamer: Outliers : 0.66 % Allowed : 6.08 % Favored : 93.26 % 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: -4.14 (0.27), residues: 838 helix: -3.87 (0.26), residues: 189 sheet: -3.67 (0.36), residues: 172 loop : -1.84 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 85 HIS 0.005 0.001 HIS A 294 PHE 0.011 0.001 PHE A 222 TYR 0.014 0.001 TYR A 198 ARG 0.005 0.000 ARG A 583 *********************** 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 62 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.767 Fit side-chains REVERT: A 611 ASP cc_start: 0.8218 (p0) cc_final: 0.7883 (p0) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.1919 time to fit residues: 15.9541 Evaluate side-chains 51 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU 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: 2.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.122654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094503 restraints weight = 10628.135| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.58 r_work: 0.2899 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7110 Z= 0.287 Angle : 0.773 9.055 9683 Z= 0.354 Chirality : 0.054 0.377 1239 Planarity : 0.005 0.050 1214 Dihedral : 16.288 112.449 1631 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 1.06 % Allowed : 11.10 % Favored : 87.85 % 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: -4.22 (0.26), residues: 838 helix: -3.94 (0.25), residues: 194 sheet: -3.70 (0.36), residues: 164 loop : -1.90 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 362 HIS 0.007 0.001 HIS A 172 PHE 0.014 0.002 PHE A 437 TYR 0.018 0.002 TYR A 198 ARG 0.005 0.000 ARG A 583 *********************** 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 59 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6074 (p0) cc_final: 0.5677 (m-40) REVERT: A 599 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7579 (tp40) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.2037 time to fit residues: 16.2275 Evaluate side-chains 49 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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: 0.0970 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.125873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097564 restraints weight = 10589.676| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.77 r_work: 0.2954 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7110 Z= 0.157 Angle : 0.672 8.271 9683 Z= 0.310 Chirality : 0.050 0.388 1239 Planarity : 0.004 0.049 1214 Dihedral : 14.810 113.196 1631 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.04 % Favored : 92.84 % Rotamer: Outliers : 1.45 % Allowed : 13.61 % Favored : 84.94 % 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: -4.14 (0.27), residues: 838 helix: -3.88 (0.26), residues: 195 sheet: -3.81 (0.35), residues: 169 loop : -1.74 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 85 HIS 0.004 0.001 HIS A 294 PHE 0.008 0.001 PHE A 222 TYR 0.011 0.001 TYR A 198 ARG 0.003 0.000 ARG A 583 *********************** 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 62 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6174 (p0) cc_final: 0.5660 (m-40) REVERT: A 90 CYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6051 (p) REVERT: A 611 ASP cc_start: 0.8258 (p0) cc_final: 0.7940 (p0) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.2102 time to fit residues: 17.6722 Evaluate side-chains 52 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 286 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 658 LEU 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: 0.0020 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 overall best weight: 0.8132 ------------------------------------------------------------------------------- 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 = 0.125939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097584 restraints weight = 10479.697| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.75 r_work: 0.2953 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7110 Z= 0.165 Angle : 0.659 8.438 9683 Z= 0.301 Chirality : 0.050 0.377 1239 Planarity : 0.004 0.049 1214 Dihedral : 13.858 114.379 1631 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 1.72 % Allowed : 15.59 % Favored : 82.69 % 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: -4.07 (0.27), residues: 838 helix: -3.86 (0.26), residues: 195 sheet: -3.69 (0.36), residues: 168 loop : -1.71 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 85 HIS 0.004 0.001 HIS A 294 PHE 0.010 0.001 PHE A 222 TYR 0.013 0.001 TYR A 198 ARG 0.002 0.000 ARG A 583 *********************** 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: 13 poor density : 48 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 47 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6861 (t) REVERT: A 77 ASN cc_start: 0.6004 (p0) cc_final: 0.5716 (m-40) REVERT: A 90 CYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6109 (p) REVERT: A 599 GLN cc_start: 0.8372 (tp-100) cc_final: 0.8005 (tp-100) REVERT: A 611 ASP cc_start: 0.8237 (p0) cc_final: 0.7892 (p0) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.2013 time to fit residues: 16.4310 Evaluate side-chains 51 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 81 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091448 restraints weight = 10761.239| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.92 r_work: 0.2798 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 7110 Z= 0.478 Angle : 0.873 9.192 9683 Z= 0.402 Chirality : 0.058 0.376 1239 Planarity : 0.005 0.047 1214 Dihedral : 13.999 115.003 1631 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.65 % Favored : 87.23 % Rotamer: Outliers : 2.25 % Allowed : 15.59 % Favored : 82.17 % 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: -4.14 (0.26), residues: 838 helix: -3.95 (0.25), residues: 192 sheet: -3.34 (0.41), residues: 148 loop : -2.04 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 85 HIS 0.010 0.002 HIS A 172 PHE 0.018 0.002 PHE A 270 TYR 0.019 0.003 TYR A 198 ARG 0.004 0.001 ARG A 619 *********************** 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 59 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.726 Fit side-chains REVERT: A 90 CYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6370 (p) REVERT: A 326 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8433 (mm) outliers start: 17 outliers final: 9 residues processed: 56 average time/residue: 0.1764 time to fit residues: 14.2603 Evaluate side-chains 50 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 525 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.123580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095621 restraints weight = 10524.328| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.59 r_work: 0.2893 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7110 Z= 0.182 Angle : 0.682 8.915 9683 Z= 0.315 Chirality : 0.051 0.377 1239 Planarity : 0.004 0.049 1214 Dihedral : 13.136 114.693 1631 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.76 % Favored : 92.12 % 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 (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: -4.07 (0.27), residues: 838 helix: -3.85 (0.26), residues: 194 sheet: -3.75 (0.36), residues: 169 loop : -1.70 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 140 *********************** 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 57 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6065 (p0) cc_final: 0.5833 (m-40) REVERT: A 85 TRP cc_start: 0.8086 (m-10) cc_final: 0.7768 (m100) REVERT: A 90 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6195 (p) REVERT: A 334 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: A 513 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7719 (mtt-85) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.2052 time to fit residues: 15.4147 Evaluate side-chains 52 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 197 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 525 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.121976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093715 restraints weight = 10639.311| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.80 r_work: 0.2871 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7110 Z= 0.279 Angle : 0.734 9.467 9683 Z= 0.338 Chirality : 0.053 0.377 1239 Planarity : 0.004 0.050 1214 Dihedral : 12.617 112.523 1631 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.62 % Favored : 89.26 % 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 (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: -4.10 (0.27), residues: 838 helix: -3.85 (0.26), residues: 194 sheet: -3.75 (0.36), residues: 169 loop : -1.73 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 85 HIS 0.006 0.001 HIS A 172 PHE 0.017 0.001 PHE A 222 TYR 0.016 0.002 TYR A 198 ARG 0.002 0.000 ARG A 619 *********************** 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 55 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.733 Fit side-chains REVERT: A 77 ASN cc_start: 0.6086 (p0) cc_final: 0.5778 (m-40) REVERT: A 85 TRP cc_start: 0.8091 (m-10) cc_final: 0.7841 (m100) REVERT: A 326 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8393 (mm) REVERT: A 334 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7851 (pm20) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1898 time to fit residues: 14.3620 Evaluate side-chains 52 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096639 restraints weight = 10655.465| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.94 r_work: 0.2934 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7110 Z= 0.163 Angle : 0.656 8.683 9683 Z= 0.303 Chirality : 0.049 0.375 1239 Planarity : 0.004 0.052 1214 Dihedral : 11.650 110.957 1631 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.80 % Favored : 93.08 % Rotamer: Outliers : 1.45 % Allowed : 17.70 % Favored : 80.85 % 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: -4.06 (0.27), residues: 838 helix: -3.82 (0.26), residues: 201 sheet: -3.74 (0.36), residues: 169 loop : -1.65 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 85 HIS 0.003 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 *********************** 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 60 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6078 (p0) cc_final: 0.5807 (m-40) REVERT: A 85 TRP cc_start: 0.8075 (m-10) cc_final: 0.7865 (m100) REVERT: A 90 CYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6224 (p) REVERT: A 326 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8264 (mm) REVERT: A 513 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7666 (mtt-85) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.1936 time to fit residues: 15.4886 Evaluate side-chains 54 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 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 90 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.126416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098206 restraints weight = 10751.763| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.94 r_work: 0.2966 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7110 Z= 0.148 Angle : 0.627 8.116 9683 Z= 0.291 Chirality : 0.048 0.373 1239 Planarity : 0.004 0.052 1214 Dihedral : 10.818 108.669 1631 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.32 % Allowed : 17.83 % Favored : 80.85 % 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: -3.94 (0.27), residues: 838 helix: -3.78 (0.27), residues: 202 sheet: -3.65 (0.37), residues: 164 loop : -1.58 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 ********************** 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 60 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6095 (p0) cc_final: 0.5852 (m-40) REVERT: A 90 CYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6148 (p) REVERT: A 326 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 475 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7756 (tp30) REVERT: A 611 ASP cc_start: 0.8195 (p0) cc_final: 0.7815 (p0) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.1857 time to fit residues: 15.1806 Evaluate side-chains 53 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.0000 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8764 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.126419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098432 restraints weight = 10633.060| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.84 r_work: 0.2967 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 0.030 7110 Z= 0.164 Angle : 0.629 8.518 9683 Z= 0.295 Chirality : 0.049 0.373 1239 Planarity : 0.004 0.051 1214 Dihedral : 10.558 106.472 1631 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.59 % Allowed : 17.83 % 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: -3.96 (0.28), residues: 838 helix: -3.78 (0.27), residues: 196 sheet: -3.66 (0.36), residues: 174 loop : -1.58 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.04 seconds wall clock time: 53 minutes 16.50 seconds (3196.50 seconds total)