Starting phenix.real_space_refine on Thu Mar 5 02:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lid_0904/03_2026/6lid_0904.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lid_0904/03_2026/6lid_0904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lid_0904/03_2026/6lid_0904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lid_0904/03_2026/6lid_0904.map" model { file = "/net/cci-nas-00/data/ceres_data/6lid_0904/03_2026/6lid_0904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lid_0904/03_2026/6lid_0904.cif" } resolution = 2.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 90 5.16 5 C 11548 2.51 5 N 2824 2.21 5 O 3496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17964 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "B" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "C" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 3.69, per 1000 atoms: 0.21 Number of scatterers: 17964 At special positions: 0 Unit cell: (81.825, 138.557, 138.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 90 16.00 P 4 15.00 O 3496 8.00 N 2824 7.00 C 11548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS B 144 " distance=2.86 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS D 144 " distance=2.95 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.04 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " 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 BETA1-4 " 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 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-ASN " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 332 " " NAG G 1 " - " ASN A 495 " " NAG H 1 " - " ASN A 513 " " NAG I 1 " - " ASN A 575 " " NAG J 1 " - " ASN C 261 " " NAG K 1 " - " ASN C 332 " " NAG L 1 " - " ASN C 495 " " NAG M 1 " - " ASN C 513 " " NAG N 1 " - " ASN C 575 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 652.6 milliseconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4048 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 54.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.581A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.841A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.514A pdb=" N ALA A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.001A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.982A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.980A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.503A pdb=" N GLN A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 395 through 398 Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.663A pdb=" N SER A 505 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.531A pdb=" N LEU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.837A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.173A pdb=" N ILE B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 50 through 57 removed outlier: 4.519A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 91 removed outlier: 3.514A pdb=" N ILE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.649A pdb=" N GLU B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.881A pdb=" N ALA B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 3.806A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 147 through 166 removed outlier: 3.678A pdb=" N VAL B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.527A pdb=" N TYR B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 176 through 202 removed outlier: 3.607A pdb=" N LYS B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.739A pdb=" N PHE B 207 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.621A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.659A pdb=" N GLN B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B 238 " --> pdb=" O TRP B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 250 through 278 Proline residue: B 261 - end of helix removed outlier: 4.168A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.709A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.520A pdb=" N THR B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 removed outlier: 3.652A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.507A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 374 through 396 removed outlier: 3.847A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 432 removed outlier: 3.511A pdb=" N SER B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 440 through 455 removed outlier: 3.726A pdb=" N GLY B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 478 Proline residue: B 468 - end of helix removed outlier: 3.510A pdb=" N MET B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.606A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.581A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.841A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 removed outlier: 3.514A pdb=" N ALA C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.001A pdb=" N GLY C 121 " --> pdb=" O TRP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.982A pdb=" N PHE C 131 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.980A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.502A pdb=" N GLN C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 395 through 398 Processing helix chain 'C' and resid 420 through 435 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.663A pdb=" N SER C 505 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.531A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'C' and resid 655 through 659 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.837A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 4.172A pdb=" N ILE D 48 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 49 " --> pdb=" O SER D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 50 through 57 removed outlier: 4.519A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 91 removed outlier: 3.513A pdb=" N ILE D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.649A pdb=" N GLU D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.882A pdb=" N ALA D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 removed outlier: 3.806A pdb=" N TYR D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 147 through 166 removed outlier: 3.678A pdb=" N VAL D 151 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.527A pdb=" N TYR D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 176 through 202 removed outlier: 3.606A pdb=" N LYS D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 229 removed outlier: 3.621A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.659A pdb=" N GLN D 237 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 238 " --> pdb=" O TRP D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 238' Processing helix chain 'D' and resid 250 through 278 Proline residue: D 261 - end of helix removed outlier: 4.168A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 removed outlier: 3.709A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.520A pdb=" N THR D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.653A pdb=" N ALA D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 325 through 333 removed outlier: 3.507A pdb=" N VAL D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 Processing helix chain 'D' and resid 374 through 396 removed outlier: 3.848A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 432 removed outlier: 3.510A pdb=" N SER D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 422 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Proline residue: D 428 - end of helix Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 440 through 455 removed outlier: 3.727A pdb=" N GLY D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 478 Proline residue: D 468 - end of helix removed outlier: 3.511A pdb=" N MET D 475 " --> pdb=" O MET D 471 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408 removed outlier: 4.077A pdb=" N PHE A 407 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 383 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 7.136A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.536A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.115A pdb=" N ILE A 329 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 632 through 634 removed outlier: 11.470A pdb=" N LYS A 617 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ASN A 651 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 649 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE A 680 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 345 Processing sheet with id=AA9, first strand: chain 'C' and resid 407 through 408 removed outlier: 4.077A pdb=" N PHE C 407 " --> pdb=" O MET C 381 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 383 " --> pdb=" O PHE C 407 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 7.135A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.537A pdb=" N GLN C 272 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 330 removed outlier: 4.114A pdb=" N ILE C 329 " --> pdb=" O TYR C 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 632 through 634 removed outlier: 11.470A pdb=" N LYS C 617 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ASN C 651 " --> pdb=" O LYS C 617 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG C 619 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU C 649 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 647 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER C 623 " --> pdb=" O GLY C 645 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY C 645 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 603 through 605 Processing sheet with id=AB6, first strand: chain 'C' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE C 680 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 344 through 345 735 hydrogen bonds defined for protein. 2082 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: 2.94 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4702 1.33 - 1.45: 3458 1.45 - 1.57: 9862 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 18172 Sorted by residual: bond pdb=" C31 3PH B 702 " pdb=" O31 3PH B 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C31 3PH D 702 " pdb=" O31 3PH D 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 3PH B 701 " pdb=" O31 3PH B 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C21 3PH D 701 " pdb=" O21 3PH D 701 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH D 701 " pdb=" O31 3PH D 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 18167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 23517 1.98 - 3.96: 923 3.96 - 5.95: 164 5.95 - 7.93: 58 7.93 - 9.91: 34 Bond angle restraints: 24696 Sorted by residual: angle pdb=" N GLU D 484 " pdb=" CA GLU D 484 " pdb=" C GLU D 484 " ideal model delta sigma weight residual 108.74 118.65 -9.91 1.38e+00 5.25e-01 5.16e+01 angle pdb=" N TYR A 175 " pdb=" CA TYR A 175 " pdb=" C TYR A 175 " ideal model delta sigma weight residual 110.91 118.92 -8.01 1.17e+00 7.31e-01 4.69e+01 angle pdb=" N TYR C 175 " pdb=" CA TYR C 175 " pdb=" C TYR C 175 " ideal model delta sigma weight residual 110.91 118.88 -7.97 1.17e+00 7.31e-01 4.64e+01 angle pdb=" N ILE D 465 " pdb=" CA ILE D 465 " pdb=" C ILE D 465 " ideal model delta sigma weight residual 111.90 106.55 5.35 8.10e-01 1.52e+00 4.37e+01 angle pdb=" N ILE B 465 " pdb=" CA ILE B 465 " pdb=" C ILE B 465 " ideal model delta sigma weight residual 111.90 106.55 5.35 8.10e-01 1.52e+00 4.36e+01 ... (remaining 24691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 10328 23.96 - 47.93: 548 47.93 - 71.89: 93 71.89 - 95.85: 19 95.85 - 119.81: 2 Dihedral angle restraints: 10990 sinusoidal: 4674 harmonic: 6316 Sorted by residual: dihedral pdb=" CA TYR A 259 " pdb=" C TYR A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA TYR C 259 " pdb=" C TYR C 259 " pdb=" N GLY C 260 " pdb=" CA GLY C 260 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 114 " pdb=" SG CYS C 114 " pdb=" SG CYS D 144 " pdb=" CB CYS D 144 " ideal model delta sinusoidal sigma weight residual 93.00 134.07 -41.07 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 10987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2768 0.146 - 0.293: 36 0.293 - 0.439: 10 0.439 - 0.585: 0 0.585 - 0.732: 4 Chirality restraints: 2818 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 261 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 513 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 2815 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 261 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 260 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO D 261 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 428 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.038 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 158 2.49 - 3.09: 11084 3.09 - 3.70: 27251 3.70 - 4.30: 43223 4.30 - 4.90: 67678 Nonbonded interactions: 149394 Sorted by model distance: nonbonded pdb=" ND1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 1.890 3.420 nonbonded pdb=" ND1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 1.894 3.420 nonbonded pdb=" CE1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 2.208 3.560 nonbonded pdb=" O PRO B 482 " pdb=" N GLU B 484 " model vdw 2.238 3.120 nonbonded pdb=" CE1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 2.238 3.560 ... (remaining 149389 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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: 0.030 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.012 0.924 18198 Z= 0.567 Angle : 1.102 38.695 24768 Z= 0.564 Chirality : 0.064 0.732 2818 Planarity : 0.007 0.081 3056 Dihedral : 15.030 119.812 6924 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 1.96 % Allowed : 3.17 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.13), residues: 2154 helix: -4.66 (0.05), residues: 998 sheet: -0.33 (0.34), residues: 182 loop : -1.96 (0.16), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.022 0.002 TYR C 65 PHE 0.023 0.002 PHE A 407 TRP 0.014 0.002 TRP B 383 HIS 0.007 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00736 (18172) covalent geometry : angle 0.99545 (24696) SS BOND : bond 0.50783 ( 6) SS BOND : angle 16.31346 ( 12) hydrogen bonds : bond 0.32346 ( 735) hydrogen bonds : angle 9.87573 ( 2082) link_BETA1-4 : bond 0.01954 ( 10) link_BETA1-4 : angle 6.46766 ( 30) link_NAG-ASN : bond 0.01296 ( 10) link_NAG-ASN : angle 6.15856 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8938 (tmm) cc_final: 0.8565 (tmm) REVERT: A 381 MET cc_start: 0.8748 (ttp) cc_final: 0.8385 (ttp) REVERT: A 432 MET cc_start: 0.9225 (mmm) cc_final: 0.9000 (mmp) REVERT: A 435 MET cc_start: 0.9140 (ptt) cc_final: 0.8870 (ptm) REVERT: B 116 SER cc_start: 0.7218 (OUTLIER) cc_final: 0.6721 (m) REVERT: B 468 PRO cc_start: 0.5965 (Cg_exo) cc_final: 0.5617 (Cg_endo) REVERT: C 357 MET cc_start: 0.8938 (tmm) cc_final: 0.8566 (tmm) REVERT: C 381 MET cc_start: 0.8747 (ttp) cc_final: 0.8380 (ttp) REVERT: C 432 MET cc_start: 0.9234 (mmm) cc_final: 0.9001 (mmp) REVERT: C 435 MET cc_start: 0.9146 (ptt) cc_final: 0.8878 (ptm) REVERT: D 116 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6566 (m) REVERT: D 194 SER cc_start: 0.7013 (p) cc_final: 0.6469 (m) outliers start: 37 outliers final: 4 residues processed: 368 average time/residue: 0.5231 time to fit residues: 217.6571 Evaluate side-chains 206 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 200 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 145 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 156 ASN A 201 HIS A 220 HIS A 324 HIS A 330 GLN A 422 ASN A 442 ASN A 493 ASN A 510 GLN A 598 ASN A 609 ASN A 625 ASN B 239 ASN B 247 ASN C 125 GLN C 156 ASN C 201 HIS C 220 HIS C 324 HIS C 330 GLN C 422 ASN C 442 ASN C 493 ASN C 510 GLN C 598 ASN C 609 ASN C 625 ASN D 239 ASN D 247 ASN D 474 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107076 restraints weight = 19149.880| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.83 r_work: 0.2903 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18198 Z= 0.210 Angle : 0.828 10.531 24768 Z= 0.407 Chirality : 0.054 0.442 2818 Planarity : 0.006 0.045 3056 Dihedral : 11.632 109.727 2962 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 2.91 % Allowed : 10.36 % Favored : 86.73 % 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 are not related in a simple way. whole: -2.48 (0.16), residues: 2154 helix: -2.07 (0.13), residues: 1008 sheet: 0.11 (0.35), residues: 180 loop : -1.34 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 296 TYR 0.019 0.002 TYR A 259 PHE 0.023 0.002 PHE C 407 TRP 0.014 0.002 TRP A 239 HIS 0.008 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00472 (18172) covalent geometry : angle 0.79732 (24696) SS BOND : bond 0.00723 ( 6) SS BOND : angle 1.10857 ( 12) hydrogen bonds : bond 0.06771 ( 735) hydrogen bonds : angle 5.05410 ( 2082) link_BETA1-4 : bond 0.01074 ( 10) link_BETA1-4 : angle 4.15284 ( 30) link_NAG-ASN : bond 0.01224 ( 10) link_NAG-ASN : angle 5.00756 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.4725 (ttp) cc_final: 0.4482 (ttm) REVERT: A 271 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8285 (t0) REVERT: A 432 MET cc_start: 0.9473 (mmm) cc_final: 0.9191 (mmp) REVERT: A 435 MET cc_start: 0.9403 (ptt) cc_final: 0.9162 (ptt) REVERT: A 542 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8944 (mtpt) REVERT: A 601 GLU cc_start: 0.7317 (pm20) cc_final: 0.6975 (mm-30) REVERT: B 134 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 180 PHE cc_start: 0.5660 (m-10) cc_final: 0.5386 (m-10) REVERT: B 181 THR cc_start: 0.6187 (OUTLIER) cc_final: 0.5882 (p) REVERT: B 194 SER cc_start: 0.7029 (p) cc_final: 0.6773 (m) REVERT: B 199 LEU cc_start: 0.7209 (tp) cc_final: 0.6796 (mt) REVERT: B 254 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.3630 (tp) REVERT: B 453 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5167 (tp) REVERT: C 271 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8233 (t0) REVERT: C 432 MET cc_start: 0.9482 (mmm) cc_final: 0.9196 (mmp) REVERT: C 435 MET cc_start: 0.9407 (ptt) cc_final: 0.9164 (ptt) REVERT: C 542 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8957 (mtpt) REVERT: C 601 GLU cc_start: 0.7333 (pm20) cc_final: 0.6960 (mm-30) REVERT: D 56 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7495 (tm) REVERT: D 134 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: D 181 THR cc_start: 0.6104 (OUTLIER) cc_final: 0.5643 (p) REVERT: D 194 SER cc_start: 0.6872 (p) cc_final: 0.6519 (m) REVERT: D 199 LEU cc_start: 0.6827 (tp) cc_final: 0.6491 (mt) REVERT: D 239 ASN cc_start: 0.5943 (OUTLIER) cc_final: 0.5512 (t0) REVERT: D 337 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5548 (tpt) REVERT: D 464 LYS cc_start: 0.4206 (OUTLIER) cc_final: 0.3717 (mmtm) outliers start: 55 outliers final: 12 residues processed: 257 average time/residue: 0.5795 time to fit residues: 167.4579 Evaluate side-chains 208 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 609 ASN A 679 ASN C 609 ASN C 679 ASN D 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110450 restraints weight = 19570.057| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.90 r_work: 0.2908 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18198 Z= 0.134 Angle : 0.707 9.693 24768 Z= 0.338 Chirality : 0.048 0.368 2818 Planarity : 0.004 0.041 3056 Dihedral : 11.088 110.638 2952 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.70 % Allowed : 12.53 % Favored : 84.78 % 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 are not related in a simple way. whole: -1.23 (0.17), residues: 2154 helix: -0.65 (0.16), residues: 1002 sheet: 0.25 (0.36), residues: 180 loop : -1.07 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 296 TYR 0.017 0.001 TYR D 377 PHE 0.015 0.001 PHE C 407 TRP 0.011 0.001 TRP C 569 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00284 (18172) covalent geometry : angle 0.67739 (24696) SS BOND : bond 0.00542 ( 6) SS BOND : angle 0.60739 ( 12) hydrogen bonds : bond 0.04981 ( 735) hydrogen bonds : angle 4.56710 ( 2082) link_BETA1-4 : bond 0.01074 ( 10) link_BETA1-4 : angle 3.84521 ( 30) link_NAG-ASN : bond 0.01225 ( 10) link_NAG-ASN : angle 4.49888 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5028 (ttp) cc_final: 0.4741 (ttp) REVERT: A 271 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8309 (t0) REVERT: A 432 MET cc_start: 0.9517 (mmm) cc_final: 0.9261 (mmp) REVERT: A 512 ASP cc_start: 0.7882 (p0) cc_final: 0.7460 (p0) REVERT: A 542 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8923 (mtpt) REVERT: B 165 VAL cc_start: 0.7567 (t) cc_final: 0.7345 (t) REVERT: B 180 PHE cc_start: 0.5577 (m-10) cc_final: 0.5282 (m-10) REVERT: B 199 LEU cc_start: 0.7095 (tp) cc_final: 0.6699 (mt) REVERT: B 254 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.3630 (tp) REVERT: B 402 GLU cc_start: 0.5875 (mp0) cc_final: 0.3981 (tp30) REVERT: B 453 LEU cc_start: 0.5847 (mp) cc_final: 0.5040 (tp) REVERT: C 271 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8305 (t0) REVERT: C 432 MET cc_start: 0.9526 (mmm) cc_final: 0.9268 (mmp) REVERT: C 512 ASP cc_start: 0.7881 (p0) cc_final: 0.7461 (p0) REVERT: C 542 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8931 (mtpt) REVERT: D 56 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7367 (tm) REVERT: D 107 ILE cc_start: 0.5451 (mt) cc_final: 0.4945 (pp) REVERT: D 134 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: D 180 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.4904 (m-10) REVERT: D 199 LEU cc_start: 0.6803 (tp) cc_final: 0.6508 (mt) REVERT: D 239 ASN cc_start: 0.5658 (OUTLIER) cc_final: 0.5327 (t0) REVERT: D 278 MET cc_start: 0.7324 (mtm) cc_final: 0.6771 (ttm) REVERT: D 360 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 442 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6149 (mt) REVERT: D 471 MET cc_start: 0.7376 (mtm) cc_final: 0.7077 (mtt) outliers start: 51 outliers final: 15 residues processed: 258 average time/residue: 0.5713 time to fit residues: 165.4513 Evaluate side-chains 215 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 180 PHE Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 679 ASN B 237 GLN C 609 ASN C 679 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.180522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112780 restraints weight = 19477.793| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.90 r_work: 0.2926 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18198 Z= 0.130 Angle : 0.688 9.755 24768 Z= 0.327 Chirality : 0.048 0.362 2818 Planarity : 0.004 0.041 3056 Dihedral : 10.694 110.379 2948 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.27 % Allowed : 13.95 % Favored : 83.77 % 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 are not related in a simple way. whole: -0.60 (0.18), residues: 2154 helix: -0.03 (0.17), residues: 1002 sheet: 0.42 (0.37), residues: 180 loop : -0.85 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 296 TYR 0.018 0.001 TYR D 377 PHE 0.016 0.001 PHE A 407 TRP 0.011 0.001 TRP D 383 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00282 (18172) covalent geometry : angle 0.65809 (24696) SS BOND : bond 0.00784 ( 6) SS BOND : angle 1.92347 ( 12) hydrogen bonds : bond 0.04309 ( 735) hydrogen bonds : angle 4.36491 ( 2082) link_BETA1-4 : bond 0.01081 ( 10) link_BETA1-4 : angle 3.67376 ( 30) link_NAG-ASN : bond 0.01166 ( 10) link_NAG-ASN : angle 4.38128 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5151 (ttp) cc_final: 0.4912 (ttp) REVERT: A 271 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8382 (t0) REVERT: A 432 MET cc_start: 0.9518 (mmm) cc_final: 0.9273 (mmp) REVERT: A 512 ASP cc_start: 0.7730 (p0) cc_final: 0.7297 (p0) REVERT: A 542 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8915 (mtpt) REVERT: A 610 MET cc_start: 0.8584 (mtp) cc_final: 0.8368 (mmt) REVERT: A 653 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8059 (mtpt) REVERT: B 134 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 165 VAL cc_start: 0.7576 (t) cc_final: 0.7368 (t) REVERT: B 180 PHE cc_start: 0.5725 (m-10) cc_final: 0.5371 (m-10) REVERT: B 199 LEU cc_start: 0.7029 (tp) cc_final: 0.6657 (mt) REVERT: B 254 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.3702 (tp) REVERT: B 278 MET cc_start: 0.7228 (mtm) cc_final: 0.6715 (ttm) REVERT: B 402 GLU cc_start: 0.5965 (mp0) cc_final: 0.4106 (tp30) REVERT: B 453 LEU cc_start: 0.5911 (mt) cc_final: 0.5098 (tp) REVERT: C 271 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8346 (t0) REVERT: C 432 MET cc_start: 0.9526 (mmm) cc_final: 0.9275 (mmp) REVERT: C 512 ASP cc_start: 0.7730 (p0) cc_final: 0.7316 (p0) REVERT: C 542 LYS cc_start: 0.9193 (mtpt) cc_final: 0.8923 (mtpt) REVERT: C 610 MET cc_start: 0.8599 (mtp) cc_final: 0.8397 (mmt) REVERT: C 653 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8073 (mtpt) REVERT: D 56 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7273 (tm) REVERT: D 85 GLU cc_start: 0.5976 (tt0) cc_final: 0.5422 (tm-30) REVERT: D 107 ILE cc_start: 0.5392 (mt) cc_final: 0.4882 (pp) REVERT: D 134 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: D 199 LEU cc_start: 0.6954 (tp) cc_final: 0.6658 (mt) REVERT: D 278 MET cc_start: 0.7328 (mtm) cc_final: 0.6678 (ttm) REVERT: D 360 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7563 (mp) REVERT: D 442 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6217 (mt) REVERT: D 471 MET cc_start: 0.7417 (mtm) cc_final: 0.7069 (mtt) outliers start: 43 outliers final: 17 residues processed: 234 average time/residue: 0.5753 time to fit residues: 150.4601 Evaluate side-chains 214 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 191 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 679 ASN B 237 GLN B 474 GLN C 609 ASN C 679 ASN D 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.180381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112956 restraints weight = 19456.527| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.82 r_work: 0.2919 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18198 Z= 0.124 Angle : 0.664 9.732 24768 Z= 0.316 Chirality : 0.048 0.359 2818 Planarity : 0.004 0.045 3056 Dihedral : 10.411 111.467 2948 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.48 % Allowed : 14.11 % Favored : 83.40 % 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 are not related in a simple way. whole: -0.16 (0.18), residues: 2154 helix: 0.43 (0.17), residues: 1004 sheet: 0.55 (0.37), residues: 180 loop : -0.73 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.018 0.001 TYR D 377 PHE 0.015 0.001 PHE C 407 TRP 0.011 0.001 TRP D 383 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00270 (18172) covalent geometry : angle 0.63607 (24696) SS BOND : bond 0.00784 ( 6) SS BOND : angle 1.23133 ( 12) hydrogen bonds : bond 0.03969 ( 735) hydrogen bonds : angle 4.27211 ( 2082) link_BETA1-4 : bond 0.01008 ( 10) link_BETA1-4 : angle 3.46636 ( 30) link_NAG-ASN : bond 0.01154 ( 10) link_NAG-ASN : angle 4.26990 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5320 (ttp) cc_final: 0.5028 (ttp) REVERT: A 271 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8400 (t0) REVERT: A 512 ASP cc_start: 0.7721 (p0) cc_final: 0.7257 (p0) REVERT: A 542 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8913 (mtpt) REVERT: A 610 MET cc_start: 0.8585 (mtp) cc_final: 0.8326 (mmt) REVERT: A 653 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8109 (mtpt) REVERT: B 134 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: B 180 PHE cc_start: 0.5617 (m-10) cc_final: 0.5205 (m-10) REVERT: B 199 LEU cc_start: 0.7045 (tp) cc_final: 0.6778 (mt) REVERT: B 254 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4004 (tp) REVERT: B 276 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7502 (t) REVERT: B 278 MET cc_start: 0.7282 (mtm) cc_final: 0.6965 (ttm) REVERT: B 284 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7283 (mt) REVERT: B 365 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: B 402 GLU cc_start: 0.6004 (mp0) cc_final: 0.4132 (tp30) REVERT: B 453 LEU cc_start: 0.5884 (mt) cc_final: 0.5674 (mm) REVERT: C 271 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8400 (t0) REVERT: C 512 ASP cc_start: 0.7705 (p0) cc_final: 0.7265 (p0) REVERT: C 542 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8902 (mtpt) REVERT: C 610 MET cc_start: 0.8570 (mtp) cc_final: 0.8312 (mmt) REVERT: C 653 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8087 (mtpt) REVERT: D 56 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7249 (tm) REVERT: D 85 GLU cc_start: 0.5795 (tt0) cc_final: 0.5316 (tm-30) REVERT: D 107 ILE cc_start: 0.5340 (mt) cc_final: 0.4898 (pp) REVERT: D 134 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: D 199 LEU cc_start: 0.6951 (tp) cc_final: 0.6695 (mt) REVERT: D 239 ASN cc_start: 0.5673 (OUTLIER) cc_final: 0.5368 (m-40) REVERT: D 278 MET cc_start: 0.7210 (mtm) cc_final: 0.6725 (ttm) REVERT: D 360 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7641 (mp) REVERT: D 442 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6131 (mt) REVERT: D 471 MET cc_start: 0.7441 (mtm) cc_final: 0.7093 (mtt) outliers start: 47 outliers final: 22 residues processed: 238 average time/residue: 0.5504 time to fit residues: 147.3518 Evaluate side-chains 226 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 67 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 679 ASN C 609 ASN C 679 ASN D 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112902 restraints weight = 19414.972| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.86 r_work: 0.2913 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18198 Z= 0.121 Angle : 0.661 9.722 24768 Z= 0.314 Chirality : 0.048 0.352 2818 Planarity : 0.004 0.049 3056 Dihedral : 10.234 111.063 2948 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.59 % Allowed : 14.59 % Favored : 82.82 % 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 are not related in a simple way. whole: 0.05 (0.18), residues: 2154 helix: 0.66 (0.17), residues: 1006 sheet: 0.57 (0.38), residues: 180 loop : -0.67 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.018 0.001 TYR D 377 PHE 0.015 0.001 PHE C 407 TRP 0.011 0.001 TRP C 569 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00263 (18172) covalent geometry : angle 0.63372 (24696) SS BOND : bond 0.00741 ( 6) SS BOND : angle 1.00328 ( 12) hydrogen bonds : bond 0.03819 ( 735) hydrogen bonds : angle 4.23810 ( 2082) link_BETA1-4 : bond 0.01006 ( 10) link_BETA1-4 : angle 3.49406 ( 30) link_NAG-ASN : bond 0.01072 ( 10) link_NAG-ASN : angle 4.23451 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5467 (ttp) cc_final: 0.5179 (ttp) REVERT: A 271 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8392 (t0) REVERT: A 512 ASP cc_start: 0.7710 (p0) cc_final: 0.7239 (p0) REVERT: A 542 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8881 (mtpt) REVERT: A 610 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8366 (mmt) REVERT: A 653 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: B 134 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: B 180 PHE cc_start: 0.5607 (m-10) cc_final: 0.5212 (m-10) REVERT: B 199 LEU cc_start: 0.7106 (tp) cc_final: 0.6855 (mt) REVERT: B 254 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.3974 (tp) REVERT: B 276 THR cc_start: 0.7715 (m) cc_final: 0.7503 (t) REVERT: B 278 MET cc_start: 0.7189 (mtm) cc_final: 0.6944 (ttm) REVERT: B 365 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: B 402 GLU cc_start: 0.6002 (mp0) cc_final: 0.4127 (tp30) REVERT: C 271 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8399 (t0) REVERT: C 512 ASP cc_start: 0.7698 (p0) cc_final: 0.7235 (p0) REVERT: C 542 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8891 (mtpt) REVERT: C 610 MET cc_start: 0.8591 (mtp) cc_final: 0.8341 (mmt) REVERT: C 653 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8117 (mtpt) REVERT: D 85 GLU cc_start: 0.5746 (tt0) cc_final: 0.5326 (tm-30) REVERT: D 107 ILE cc_start: 0.5495 (mt) cc_final: 0.5066 (pp) REVERT: D 134 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: D 199 LEU cc_start: 0.6936 (tp) cc_final: 0.6683 (mt) REVERT: D 278 MET cc_start: 0.7161 (mtm) cc_final: 0.6780 (ttm) REVERT: D 360 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7566 (mp) REVERT: D 442 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6144 (mt) REVERT: D 464 LYS cc_start: 0.4178 (OUTLIER) cc_final: 0.3845 (mmtp) REVERT: D 471 MET cc_start: 0.7585 (mtm) cc_final: 0.7197 (mtt) outliers start: 49 outliers final: 17 residues processed: 230 average time/residue: 0.5575 time to fit residues: 144.0746 Evaluate side-chains 221 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 150 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN B 474 GLN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109051 restraints weight = 19459.039| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.69 r_work: 0.2968 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18198 Z= 0.125 Angle : 0.661 9.759 24768 Z= 0.313 Chirality : 0.048 0.353 2818 Planarity : 0.004 0.050 3056 Dihedral : 10.079 109.192 2948 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.33 % Allowed : 14.96 % Favored : 82.72 % 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 are not related in a simple way. whole: 0.18 (0.18), residues: 2154 helix: 0.78 (0.17), residues: 1010 sheet: 0.58 (0.38), residues: 180 loop : -0.61 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.017 0.001 TYR D 377 PHE 0.017 0.001 PHE A 407 TRP 0.011 0.001 TRP A 239 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00276 (18172) covalent geometry : angle 0.63429 (24696) SS BOND : bond 0.00555 ( 6) SS BOND : angle 0.92307 ( 12) hydrogen bonds : bond 0.03853 ( 735) hydrogen bonds : angle 4.21040 ( 2082) link_BETA1-4 : bond 0.00999 ( 10) link_BETA1-4 : angle 3.38093 ( 30) link_NAG-ASN : bond 0.01033 ( 10) link_NAG-ASN : angle 4.21767 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5846 (ttp) cc_final: 0.5223 (ttp) REVERT: A 271 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8390 (t0) REVERT: A 512 ASP cc_start: 0.7656 (p0) cc_final: 0.7184 (p0) REVERT: A 542 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8840 (mtpt) REVERT: A 610 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8249 (mmt) REVERT: A 653 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8144 (mtpt) REVERT: B 134 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 180 PHE cc_start: 0.5722 (m-10) cc_final: 0.5363 (m-10) REVERT: B 199 LEU cc_start: 0.7077 (tp) cc_final: 0.6835 (mt) REVERT: B 254 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.3506 (tp) REVERT: B 276 THR cc_start: 0.7627 (m) cc_final: 0.7419 (t) REVERT: B 278 MET cc_start: 0.7053 (mtm) cc_final: 0.6844 (ttm) REVERT: B 323 THR cc_start: 0.5548 (OUTLIER) cc_final: 0.5193 (p) REVERT: B 365 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: B 402 GLU cc_start: 0.5938 (mp0) cc_final: 0.4014 (tp30) REVERT: B 453 LEU cc_start: 0.5366 (mm) cc_final: 0.4666 (tp) REVERT: C 271 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8354 (t0) REVERT: C 512 ASP cc_start: 0.7654 (p0) cc_final: 0.7175 (p0) REVERT: C 542 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8843 (mtpt) REVERT: C 610 MET cc_start: 0.8528 (mtp) cc_final: 0.8236 (mmt) REVERT: C 653 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8157 (mtpt) REVERT: D 85 GLU cc_start: 0.5704 (tt0) cc_final: 0.5333 (tm-30) REVERT: D 107 ILE cc_start: 0.5479 (mt) cc_final: 0.5038 (pp) REVERT: D 134 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: D 199 LEU cc_start: 0.6915 (tp) cc_final: 0.6667 (mt) REVERT: D 263 VAL cc_start: 0.6238 (OUTLIER) cc_final: 0.5827 (p) REVERT: D 278 MET cc_start: 0.7102 (mtm) cc_final: 0.6696 (ttm) REVERT: D 323 THR cc_start: 0.5550 (OUTLIER) cc_final: 0.5179 (p) REVERT: D 442 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6168 (mt) REVERT: D 464 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3854 (mmtp) REVERT: D 471 MET cc_start: 0.7613 (mtm) cc_final: 0.7204 (mtt) outliers start: 44 outliers final: 16 residues processed: 236 average time/residue: 0.5465 time to fit residues: 145.0537 Evaluate side-chains 219 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110893 restraints weight = 19276.538| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.65 r_work: 0.2945 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18198 Z= 0.135 Angle : 0.665 10.681 24768 Z= 0.317 Chirality : 0.048 0.358 2818 Planarity : 0.004 0.054 3056 Dihedral : 10.031 109.055 2948 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.33 % Allowed : 15.33 % Favored : 82.35 % 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 are not related in a simple way. whole: 0.23 (0.18), residues: 2154 helix: 0.84 (0.17), residues: 1010 sheet: 0.58 (0.38), residues: 180 loop : -0.60 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.017 0.001 TYR D 377 PHE 0.018 0.001 PHE C 407 TRP 0.011 0.001 TRP C 239 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00306 (18172) covalent geometry : angle 0.63861 (24696) SS BOND : bond 0.00616 ( 6) SS BOND : angle 0.95264 ( 12) hydrogen bonds : bond 0.03944 ( 735) hydrogen bonds : angle 4.24907 ( 2082) link_BETA1-4 : bond 0.00955 ( 10) link_BETA1-4 : angle 3.33473 ( 30) link_NAG-ASN : bond 0.01006 ( 10) link_NAG-ASN : angle 4.21711 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5957 (ttp) cc_final: 0.5614 (ttp) REVERT: A 271 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8363 (t0) REVERT: A 512 ASP cc_start: 0.7702 (p0) cc_final: 0.7210 (p0) REVERT: A 542 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8858 (mtpt) REVERT: A 610 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8304 (mmt) REVERT: A 653 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8150 (mtpt) REVERT: B 134 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 180 PHE cc_start: 0.5599 (m-10) cc_final: 0.5249 (m-10) REVERT: B 199 LEU cc_start: 0.7115 (tp) cc_final: 0.6906 (mt) REVERT: B 254 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.3527 (tp) REVERT: B 323 THR cc_start: 0.5586 (OUTLIER) cc_final: 0.5231 (p) REVERT: B 365 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: B 402 GLU cc_start: 0.5949 (mp0) cc_final: 0.3966 (tp30) REVERT: C 271 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8381 (t0) REVERT: C 512 ASP cc_start: 0.7711 (p0) cc_final: 0.7226 (p0) REVERT: C 542 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8845 (mtpt) REVERT: C 610 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (mmt) REVERT: C 653 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8159 (mtpt) REVERT: D 85 GLU cc_start: 0.5612 (tt0) cc_final: 0.5385 (tm-30) REVERT: D 107 ILE cc_start: 0.5505 (mt) cc_final: 0.5079 (pp) REVERT: D 134 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: D 263 VAL cc_start: 0.6269 (OUTLIER) cc_final: 0.5927 (p) REVERT: D 276 THR cc_start: 0.7657 (m) cc_final: 0.7447 (t) REVERT: D 278 MET cc_start: 0.7106 (mtm) cc_final: 0.6704 (ttm) REVERT: D 323 THR cc_start: 0.5563 (OUTLIER) cc_final: 0.5206 (p) REVERT: D 442 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6177 (mt) REVERT: D 464 LYS cc_start: 0.4006 (OUTLIER) cc_final: 0.3646 (mmtp) REVERT: D 471 MET cc_start: 0.7628 (mtm) cc_final: 0.7208 (mtt) outliers start: 44 outliers final: 17 residues processed: 225 average time/residue: 0.5532 time to fit residues: 140.3650 Evaluate side-chains 215 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 213 optimal weight: 0.0770 chunk 121 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114080 restraints weight = 19218.728| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.75 r_work: 0.2981 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18198 Z= 0.117 Angle : 0.656 11.434 24768 Z= 0.309 Chirality : 0.047 0.344 2818 Planarity : 0.004 0.053 3056 Dihedral : 9.879 107.341 2948 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.38 % Allowed : 15.27 % Favored : 82.35 % 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 are not related in a simple way. whole: 0.30 (0.18), residues: 2154 helix: 0.89 (0.17), residues: 1010 sheet: 0.61 (0.38), residues: 180 loop : -0.54 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 665 TYR 0.018 0.001 TYR D 377 PHE 0.023 0.001 PHE B 459 TRP 0.011 0.001 TRP A 239 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00256 (18172) covalent geometry : angle 0.62997 (24696) SS BOND : bond 0.00744 ( 6) SS BOND : angle 2.17085 ( 12) hydrogen bonds : bond 0.03591 ( 735) hydrogen bonds : angle 4.20434 ( 2082) link_BETA1-4 : bond 0.00930 ( 10) link_BETA1-4 : angle 3.19704 ( 30) link_NAG-ASN : bond 0.01005 ( 10) link_NAG-ASN : angle 4.08474 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.6185 (ttp) cc_final: 0.5841 (ttp) REVERT: A 271 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8358 (t0) REVERT: A 512 ASP cc_start: 0.7606 (p0) cc_final: 0.7101 (p0) REVERT: A 610 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8275 (mmt) REVERT: A 653 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8121 (mtpt) REVERT: B 134 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 199 LEU cc_start: 0.7149 (tp) cc_final: 0.6925 (mt) REVERT: B 254 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.3543 (tp) REVERT: B 323 THR cc_start: 0.5616 (OUTLIER) cc_final: 0.5262 (p) REVERT: B 365 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: B 402 GLU cc_start: 0.5857 (mp0) cc_final: 0.3909 (tp30) REVERT: B 442 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6134 (mt) REVERT: B 453 LEU cc_start: 0.6010 (mp) cc_final: 0.5172 (tp) REVERT: B 467 LYS cc_start: 0.6677 (mttm) cc_final: 0.6302 (mmmt) REVERT: C 271 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8347 (t0) REVERT: C 512 ASP cc_start: 0.7601 (p0) cc_final: 0.7226 (p0) REVERT: C 610 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (mmt) REVERT: C 653 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8162 (mtpt) REVERT: D 85 GLU cc_start: 0.5657 (tt0) cc_final: 0.5433 (tm-30) REVERT: D 107 ILE cc_start: 0.5482 (mt) cc_final: 0.5033 (pp) REVERT: D 134 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: D 263 VAL cc_start: 0.6341 (OUTLIER) cc_final: 0.5873 (p) REVERT: D 278 MET cc_start: 0.7040 (mtm) cc_final: 0.6695 (ttm) REVERT: D 323 THR cc_start: 0.5587 (OUTLIER) cc_final: 0.5292 (p) REVERT: D 442 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6157 (mt) REVERT: D 464 LYS cc_start: 0.3864 (OUTLIER) cc_final: 0.3500 (mmtp) REVERT: D 471 MET cc_start: 0.7622 (mtm) cc_final: 0.7203 (mtt) outliers start: 45 outliers final: 16 residues processed: 222 average time/residue: 0.5457 time to fit residues: 136.6220 Evaluate side-chains 218 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112813 restraints weight = 19196.088| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.63 r_work: 0.2962 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18198 Z= 0.122 Angle : 0.657 10.194 24768 Z= 0.312 Chirality : 0.047 0.355 2818 Planarity : 0.004 0.052 3056 Dihedral : 9.820 107.059 2948 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.01 % Allowed : 15.64 % Favored : 82.35 % 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 are not related in a simple way. whole: 0.33 (0.18), residues: 2154 helix: 0.89 (0.17), residues: 1012 sheet: 0.63 (0.38), residues: 180 loop : -0.51 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 665 TYR 0.018 0.001 TYR D 377 PHE 0.016 0.001 PHE A 407 TRP 0.011 0.001 TRP C 239 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00271 (18172) covalent geometry : angle 0.63149 (24696) SS BOND : bond 0.00641 ( 6) SS BOND : angle 1.75252 ( 12) hydrogen bonds : bond 0.03686 ( 735) hydrogen bonds : angle 4.20302 ( 2082) link_BETA1-4 : bond 0.00902 ( 10) link_BETA1-4 : angle 3.12649 ( 30) link_NAG-ASN : bond 0.00999 ( 10) link_NAG-ASN : angle 4.10477 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.6178 (ttp) cc_final: 0.5665 (ttp) REVERT: A 271 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8271 (t0) REVERT: A 512 ASP cc_start: 0.7672 (p0) cc_final: 0.7132 (p0) REVERT: A 610 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8268 (mmt) REVERT: A 653 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8159 (mtpt) REVERT: B 134 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: B 180 PHE cc_start: 0.5660 (m-80) cc_final: 0.5368 (m-10) REVERT: B 199 LEU cc_start: 0.7125 (tp) cc_final: 0.6866 (mt) REVERT: B 254 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.3536 (tp) REVERT: B 323 THR cc_start: 0.5764 (OUTLIER) cc_final: 0.5409 (p) REVERT: B 365 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: B 402 GLU cc_start: 0.5849 (mp0) cc_final: 0.3905 (tp30) REVERT: B 442 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6134 (mt) REVERT: B 453 LEU cc_start: 0.6013 (mp) cc_final: 0.5202 (tp) REVERT: B 467 LYS cc_start: 0.6728 (mttm) cc_final: 0.6321 (tppt) REVERT: B 480 VAL cc_start: 0.5576 (m) cc_final: 0.5347 (p) REVERT: C 271 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8291 (t0) REVERT: C 512 ASP cc_start: 0.7656 (p0) cc_final: 0.7122 (p0) REVERT: C 610 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (mmt) REVERT: C 653 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8139 (mtpt) REVERT: D 85 GLU cc_start: 0.5642 (tt0) cc_final: 0.5392 (tm-30) REVERT: D 107 ILE cc_start: 0.5522 (mt) cc_final: 0.5111 (pp) REVERT: D 134 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: D 263 VAL cc_start: 0.6326 (OUTLIER) cc_final: 0.5865 (p) REVERT: D 278 MET cc_start: 0.6779 (mtm) cc_final: 0.6573 (ttm) REVERT: D 323 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.5268 (p) REVERT: D 442 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6238 (mt) REVERT: D 464 LYS cc_start: 0.3915 (OUTLIER) cc_final: 0.3567 (mmtp) REVERT: D 471 MET cc_start: 0.7616 (mtm) cc_final: 0.7199 (mtt) outliers start: 38 outliers final: 16 residues processed: 217 average time/residue: 0.5569 time to fit residues: 135.6145 Evaluate side-chains 217 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 52 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115437 restraints weight = 19246.398| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.77 r_work: 0.2929 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18198 Z= 0.132 Angle : 0.672 10.795 24768 Z= 0.318 Chirality : 0.048 0.354 2818 Planarity : 0.004 0.052 3056 Dihedral : 9.837 107.272 2948 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.06 % Allowed : 15.70 % Favored : 82.24 % 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 are not related in a simple way. whole: 0.33 (0.18), residues: 2154 helix: 0.89 (0.17), residues: 1012 sheet: 0.61 (0.38), residues: 180 loop : -0.51 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.019 0.001 TYR D 377 PHE 0.020 0.001 PHE D 459 TRP 0.011 0.001 TRP A 239 HIS 0.008 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00299 (18172) covalent geometry : angle 0.64765 (24696) SS BOND : bond 0.00651 ( 6) SS BOND : angle 1.62194 ( 12) hydrogen bonds : bond 0.03788 ( 735) hydrogen bonds : angle 4.20146 ( 2082) link_BETA1-4 : bond 0.00877 ( 10) link_BETA1-4 : angle 3.10918 ( 30) link_NAG-ASN : bond 0.00984 ( 10) link_NAG-ASN : angle 4.11191 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6820.06 seconds wall clock time: 117 minutes 5.05 seconds (7025.05 seconds total)