Starting phenix.real_space_refine on Sat Sep 12 20:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lid_0904/09_2026/6lid_0904.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lid_0904/09_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_0904/09_2026/6lid_0904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lid_0904/09_2026/6lid_0904.map" model { file = "/net/cci-nas-00/data/ceres_data/6lid_0904/09_2026/6lid_0904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lid_0904/09_2026/6lid_0904.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6lid_0904/09_2026/6lid_0904.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lid_0904/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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: 3.77, 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: 1.50 Conformation dependent library (CDL) restraints added in 560.3 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: 0.55 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: 2.71 Time building geometry restraints manager: 2.00 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 - 18.00: 9546 18.00 - 36.00: 793 36.00 - 53.99: 141 53.99 - 71.99: 41 71.99 - 89.99: 13 Dihedral angle restraints: 10534 sinusoidal: 4218 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 10531 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 14.178 89.990 6468 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/Z covalent geometry : bond 0.00736 / 0.33 (18172) covalent geometry : angle 0.99545 / 0.53 (24696) SS BOND : bond 0.50783 / 26.00 ( 6) SS BOND : angle 16.31346 / 8.07 ( 12) hydrogen bonds : bond 0.32346 / 20.73 ( 735) hydrogen bonds : angle 9.87573 / 6.86 ( 2082) link_BETA1-4 : bond 0.01954 / 0.99 ( 10) link_BETA1-4 : angle 6.46766 / 4.24 ( 30) link_NAG-ASN : bond 0.01296 / 0.60 ( 10) link_NAG-ASN : angle 6.15856 / 3.95 ( 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 : 0.665 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: 0.5159 time to fit residues: 215.5605 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 : 0.529 ------------------------------------------------------------------------------- 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: 5.9990 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... 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 = 0.4020 r_free = 0.4020 target = 0.178989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111532 restraints weight = 19180.854| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.90 r_work: 0.2931 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2267 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= 0.209 Angle : 0.814 10.908 24768 Z= 0.401 Chirality : 0.053 0.408 2818 Planarity : 0.006 0.045 3056 Dihedral : 7.780 59.915 2506 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.91 % Allowed : 10.47 % Favored : 86.63 % 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: -2.54 (0.16), residues: 2154 helix: -2.16 (0.13), residues: 1008 sheet: 0.10 (0.35), residues: 180 loop : -1.33 (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 C 239 HIS 0.008 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (18172) covalent geometry : angle 0.78718 / 0.39 (24696) SS BOND : bond 0.01700 / 0.85 ( 6) SS BOND : angle 1.09410 / 0.64 ( 12) hydrogen bonds : bond 0.06829 / 4.38 ( 735) hydrogen bonds : angle 5.07169 / 3.54 ( 2082) link_BETA1-4 : bond 0.00952 / 0.49 ( 10) link_BETA1-4 : angle 3.80514 / 2.42 ( 30) link_NAG-ASN : bond 0.01123 / 0.52 ( 10) link_NAG-ASN : angle 4.72448 / 3.05 ( 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 276 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.4816 (ttp) cc_final: 0.4583 (ttm) REVERT: A 271 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8260 (t0) REVERT: A 432 MET cc_start: 0.9475 (mmm) cc_final: 0.9257 (mmp) REVERT: A 435 MET cc_start: 0.9403 (ptt) cc_final: 0.9158 (ptt) REVERT: A 542 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8953 (mtpt) REVERT: A 601 GLU cc_start: 0.7334 (pm20) cc_final: 0.7027 (mm-30) REVERT: A 610 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8275 (mmt) REVERT: B 134 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 180 PHE cc_start: 0.5714 (m-10) cc_final: 0.5449 (m-10) REVERT: B 181 THR cc_start: 0.6289 (OUTLIER) cc_final: 0.5984 (p) REVERT: B 194 SER cc_start: 0.7048 (p) cc_final: 0.6809 (m) REVERT: B 199 LEU cc_start: 0.7235 (tp) cc_final: 0.6831 (mt) REVERT: B 254 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.3661 (tp) REVERT: B 453 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5172 (tp) REVERT: C 271 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8251 (t0) REVERT: C 432 MET cc_start: 0.9483 (mmm) cc_final: 0.9264 (mmp) REVERT: C 435 MET cc_start: 0.9409 (ptt) cc_final: 0.9164 (ptt) REVERT: C 542 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8951 (mtpt) REVERT: C 601 GLU cc_start: 0.7371 (pm20) cc_final: 0.7027 (mm-30) REVERT: C 610 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8282 (mmt) REVERT: D 56 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7573 (tm) REVERT: D 134 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: D 181 THR cc_start: 0.6143 (OUTLIER) cc_final: 0.5685 (p) REVERT: D 194 SER cc_start: 0.6904 (p) cc_final: 0.6550 (m) REVERT: D 199 LEU cc_start: 0.6857 (tp) cc_final: 0.6536 (mt) REVERT: D 239 ASN cc_start: 0.5958 (OUTLIER) cc_final: 0.5529 (t0) REVERT: D 337 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5584 (tpt) REVERT: D 464 LYS cc_start: 0.4237 (OUTLIER) cc_final: 0.3692 (mmtm) outliers start: 55 outliers final: 10 residues processed: 256 average time/residue: 0.5490 time to fit residues: 158.2810 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 107 ILE 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 C residue 610 MET Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 107 ILE 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: 0.9990 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4024 r_free = 0.4024 target = 0.179450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108843 restraints weight = 19503.570| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.83 r_work: 0.2915 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18198 Z= 0.151 Angle : 0.719 9.715 24768 Z= 0.347 Chirality : 0.049 0.332 2818 Planarity : 0.005 0.041 3056 Dihedral : 7.373 57.652 2496 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.75 % Allowed : 12.79 % Favored : 84.46 % 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: -1.29 (0.17), residues: 2154 helix: -0.72 (0.16), residues: 1002 sheet: 0.23 (0.36), residues: 180 loop : -1.09 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 296 TYR 0.016 0.001 TYR C 259 PHE 0.017 0.001 PHE C 407 TRP 0.014 0.002 TRP A 239 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (18172) covalent geometry : angle 0.69285 / 0.34 (24696) SS BOND : bond 0.00902 / 0.42 ( 6) SS BOND : angle 1.27306 / 0.75 ( 12) hydrogen bonds : bond 0.05193 / 3.33 ( 735) hydrogen bonds : angle 4.60134 / 3.21 ( 2082) link_BETA1-4 : bond 0.01042 / 0.51 ( 10) link_BETA1-4 : angle 3.53838 / 2.25 ( 30) link_NAG-ASN : bond 0.01126 / 0.52 ( 10) link_NAG-ASN : angle 4.26949 / 2.77 ( 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 268 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.4992 (ttp) cc_final: 0.4701 (ttp) REVERT: A 271 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 432 MET cc_start: 0.9512 (mmm) cc_final: 0.9260 (mmp) REVERT: A 512 ASP cc_start: 0.7741 (p0) cc_final: 0.7331 (p0) REVERT: A 542 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8922 (mtpt) REVERT: A 610 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8199 (mmt) REVERT: B 180 PHE cc_start: 0.5517 (m-10) cc_final: 0.5221 (m-10) REVERT: B 199 LEU cc_start: 0.7116 (tp) cc_final: 0.6719 (mt) REVERT: B 254 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.3616 (tp) REVERT: B 402 GLU cc_start: 0.5876 (mp0) cc_final: 0.3983 (tp30) REVERT: B 453 LEU cc_start: 0.5846 (mp) cc_final: 0.5039 (tp) REVERT: C 271 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8340 (t0) REVERT: C 432 MET cc_start: 0.9520 (mmm) cc_final: 0.9265 (mmp) REVERT: C 512 ASP cc_start: 0.7729 (p0) cc_final: 0.7332 (p0) REVERT: C 542 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8935 (mtpt) REVERT: C 610 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8229 (mmt) REVERT: D 107 ILE cc_start: 0.5310 (mt) cc_final: 0.4865 (pp) REVERT: D 134 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: D 199 LEU cc_start: 0.6984 (tp) cc_final: 0.6660 (mt) REVERT: D 239 ASN cc_start: 0.5585 (OUTLIER) cc_final: 0.5354 (t0) REVERT: D 360 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7449 (mp) REVERT: D 442 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6132 (mt) REVERT: D 471 MET cc_start: 0.7329 (mtm) cc_final: 0.7067 (mtt) outliers start: 52 outliers final: 18 residues processed: 253 average time/residue: 0.5589 time to fit residues: 159.7010 Evaluate side-chains 217 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 437 GLU Chi-restraints excluded: chain A residue 610 MET 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 C residue 437 GLU Chi-restraints excluded: chain C residue 610 MET 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 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: 0.9990 chunk 93 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 679 ASN C 609 ASN C 679 ASN D 237 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.180047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109935 restraints weight = 19499.831| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.85 r_work: 0.2917 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18198 Z= 0.128 Angle : 0.682 9.657 24768 Z= 0.325 Chirality : 0.047 0.318 2818 Planarity : 0.004 0.041 3056 Dihedral : 7.106 56.728 2492 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.22 % Allowed : 13.79 % Favored : 83.99 % 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: -0.63 (0.18), residues: 2154 helix: -0.04 (0.17), residues: 1002 sheet: 0.41 (0.37), residues: 180 loop : -0.89 (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 0.015 0.001 PHE A 407 TRP 0.011 0.001 TRP A 239 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (18172) covalent geometry : angle 0.65809 / 0.32 (24696) SS BOND : bond 0.00948 / 0.44 ( 6) SS BOND : angle 1.63058 / 1.00 ( 12) hydrogen bonds : bond 0.04312 / 2.75 ( 735) hydrogen bonds : angle 4.38603 / 3.07 ( 2082) link_BETA1-4 : bond 0.01011 / 0.50 ( 10) link_BETA1-4 : angle 3.31096 / 2.09 ( 30) link_NAG-ASN : bond 0.01073 / 0.50 ( 10) link_NAG-ASN : angle 3.99202 / 2.56 ( 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 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5224 (ttp) cc_final: 0.4985 (ttp) REVERT: A 271 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8381 (t0) REVERT: A 432 MET cc_start: 0.9506 (mmm) cc_final: 0.9253 (mmp) REVERT: A 512 ASP cc_start: 0.7711 (p0) cc_final: 0.7267 (p0) REVERT: A 542 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8889 (mtpt) REVERT: A 653 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: B 134 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 180 PHE cc_start: 0.5664 (m-10) cc_final: 0.5311 (m-10) REVERT: B 199 LEU cc_start: 0.7028 (tp) cc_final: 0.6655 (mt) REVERT: B 254 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.3762 (tp) REVERT: B 278 MET cc_start: 0.7176 (mtm) cc_final: 0.6621 (ttm) REVERT: B 402 GLU cc_start: 0.6002 (mp0) cc_final: 0.4133 (tp30) REVERT: B 453 LEU cc_start: 0.5887 (mt) cc_final: 0.5098 (tp) REVERT: C 271 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8369 (t0) REVERT: C 432 MET cc_start: 0.9514 (mmm) cc_final: 0.9261 (mmp) REVERT: C 512 ASP cc_start: 0.7705 (p0) cc_final: 0.7277 (p0) REVERT: C 542 LYS cc_start: 0.9175 (mtpt) cc_final: 0.8899 (mtpt) REVERT: C 653 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: D 85 GLU cc_start: 0.5954 (tt0) cc_final: 0.5406 (tm-30) REVERT: D 107 ILE cc_start: 0.5307 (mt) cc_final: 0.4830 (pp) REVERT: D 134 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: D 199 LEU cc_start: 0.6956 (tp) cc_final: 0.6644 (mt) REVERT: D 360 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7447 (mp) REVERT: D 442 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6196 (mt) REVERT: D 464 LYS cc_start: 0.4251 (OUTLIER) cc_final: 0.3841 (mmtt) REVERT: D 471 MET cc_start: 0.7420 (mtm) cc_final: 0.7093 (mtt) outliers start: 42 outliers final: 19 residues processed: 235 average time/residue: 0.5328 time to fit residues: 141.1154 Evaluate side-chains 223 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 437 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 134 GLU 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 Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4034 r_free = 0.4034 target = 0.180266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110658 restraints weight = 19447.778| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.81 r_work: 0.2944 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18198 Z= 0.121 Angle : 0.655 9.616 24768 Z= 0.312 Chirality : 0.047 0.311 2818 Planarity : 0.004 0.045 3056 Dihedral : 6.894 57.355 2492 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.59 % Allowed : 13.79 % Favored : 83.62 % 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: -0.12 (0.18), residues: 2154 helix: 0.45 (0.17), residues: 1012 sheet: 0.54 (0.37), residues: 180 loop : -0.69 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.017 0.001 TYR D 377 PHE 0.014 0.001 PHE C 407 TRP 0.011 0.001 TRP C 239 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18172) covalent geometry : angle 0.63249 / 0.31 (24696) SS BOND : bond 0.00558 / 0.27 ( 6) SS BOND : angle 0.98944 / 0.60 ( 12) hydrogen bonds : bond 0.03870 / 2.48 ( 735) hydrogen bonds : angle 4.25982 / 2.99 ( 2082) link_BETA1-4 : bond 0.00958 / 0.47 ( 10) link_BETA1-4 : angle 3.16893 / 2.00 ( 30) link_NAG-ASN : bond 0.00989 / 0.46 ( 10) link_NAG-ASN : angle 3.77461 / 2.44 ( 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 264 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5328 (ttp) cc_final: 0.4800 (ttp) REVERT: A 271 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8408 (t0) REVERT: A 512 ASP cc_start: 0.7635 (p0) cc_final: 0.7168 (p0) REVERT: A 542 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8861 (mtpt) REVERT: A 610 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8293 (mmt) REVERT: A 653 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8111 (mtpt) REVERT: B 134 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: B 180 PHE cc_start: 0.5626 (m-10) cc_final: 0.5233 (m-10) REVERT: B 199 LEU cc_start: 0.6993 (tp) cc_final: 0.6715 (mt) REVERT: B 254 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.3975 (tp) REVERT: B 276 THR cc_start: 0.7667 (m) cc_final: 0.7450 (t) REVERT: B 278 MET cc_start: 0.7144 (mtm) cc_final: 0.6837 (ttm) REVERT: B 365 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7424 (m-10) REVERT: B 402 GLU cc_start: 0.5918 (mp0) cc_final: 0.4109 (tp30) REVERT: C 271 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8410 (t0) REVERT: C 512 ASP cc_start: 0.7630 (p0) cc_final: 0.7183 (p0) REVERT: C 542 LYS cc_start: 0.9161 (mtpt) cc_final: 0.8872 (mtpt) REVERT: C 610 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8296 (mmt) REVERT: C 653 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8077 (mtpt) REVERT: D 85 GLU cc_start: 0.5779 (tt0) cc_final: 0.5366 (tm-30) REVERT: D 107 ILE cc_start: 0.5288 (mt) cc_final: 0.4876 (pp) REVERT: D 134 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: D 199 LEU cc_start: 0.6911 (tp) cc_final: 0.6693 (mt) REVERT: D 239 ASN cc_start: 0.5500 (OUTLIER) cc_final: 0.5280 (m-40) REVERT: D 276 THR cc_start: 0.7751 (m) cc_final: 0.7543 (t) REVERT: D 360 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 442 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6134 (mt) REVERT: D 464 LYS cc_start: 0.4282 (OUTLIER) cc_final: 0.3920 (mmtp) REVERT: D 471 MET cc_start: 0.7549 (mtm) cc_final: 0.7261 (mtt) outliers start: 49 outliers final: 17 residues processed: 247 average time/residue: 0.5341 time to fit residues: 149.5217 Evaluate side-chains 227 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 193 ILE 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 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 610 MET 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 239 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 67 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 145 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 ASN A 609 ASN A 679 ASN C 459 ASN 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 = 0.4028 r_free = 0.4028 target = 0.179735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109700 restraints weight = 19362.773| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.76 r_work: 0.2952 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3234 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= 0.131 Angle : 0.673 9.932 24768 Z= 0.320 Chirality : 0.048 0.296 2818 Planarity : 0.004 0.049 3056 Dihedral : 6.901 57.704 2492 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.64 % Allowed : 14.32 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2154 helix: 0.67 (0.17), residues: 1004 sheet: 0.55 (0.38), residues: 180 loop : -0.70 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 665 TYR 0.018 0.001 TYR D 377 PHE 0.017 0.001 PHE C 407 TRP 0.011 0.001 TRP C 239 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (18172) covalent geometry : angle 0.65146 / 0.31 (24696) SS BOND : bond 0.00719 / 0.35 ( 6) SS BOND : angle 1.03905 / 0.59 ( 12) hydrogen bonds : bond 0.03951 / 2.52 ( 735) hydrogen bonds : angle 4.28400 / 3.00 ( 2082) link_BETA1-4 : bond 0.00948 / 0.46 ( 10) link_BETA1-4 : angle 3.16738 / 2.00 ( 30) link_NAG-ASN : bond 0.00948 / 0.44 ( 10) link_NAG-ASN : angle 3.79516 / 2.46 ( 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 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8389 (t0) REVERT: A 512 ASP cc_start: 0.7691 (p0) cc_final: 0.7199 (p0) REVERT: A 610 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8256 (mmt) REVERT: A 653 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8059 (mtpt) REVERT: B 134 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: B 180 PHE cc_start: 0.5607 (m-10) cc_final: 0.5217 (m-10) REVERT: B 199 LEU cc_start: 0.7005 (tp) cc_final: 0.6728 (mt) REVERT: B 254 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.3969 (tp) REVERT: B 276 THR cc_start: 0.7671 (m) cc_final: 0.7467 (t) REVERT: B 278 MET cc_start: 0.7096 (mtm) cc_final: 0.6819 (ttm) REVERT: B 365 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: B 402 GLU cc_start: 0.5984 (mp0) cc_final: 0.4143 (tp30) REVERT: C 271 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8397 (t0) REVERT: C 512 ASP cc_start: 0.7694 (p0) cc_final: 0.7214 (p0) REVERT: C 542 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8843 (mtpt) REVERT: C 610 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8258 (mmt) REVERT: C 653 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8075 (mtpt) REVERT: D 85 GLU cc_start: 0.5728 (tt0) cc_final: 0.5255 (tm-30) REVERT: D 107 ILE cc_start: 0.5446 (mt) cc_final: 0.5048 (pp) REVERT: D 134 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: D 199 LEU cc_start: 0.6905 (tp) cc_final: 0.6693 (mt) REVERT: D 360 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7447 (mp) REVERT: D 442 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6154 (mt) REVERT: D 464 LYS cc_start: 0.4342 (OUTLIER) cc_final: 0.3865 (mmtp) REVERT: D 471 MET cc_start: 0.7572 (mtm) cc_final: 0.7237 (mtt) outliers start: 50 outliers final: 21 residues processed: 230 average time/residue: 0.5348 time to fit residues: 139.1238 Evaluate side-chains 224 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 365 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU 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 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 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 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: 5.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 105 optimal weight: 0.0020 chunk 151 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4035 r_free = 0.4035 target = 0.180330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111688 restraints weight = 19423.000| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.71 r_work: 0.2933 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18198 Z= 0.120 Angle : 0.644 9.604 24768 Z= 0.307 Chirality : 0.047 0.295 2818 Planarity : 0.004 0.049 3056 Dihedral : 6.774 58.185 2492 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.80 % Allowed : 14.69 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2154 helix: 0.75 (0.17), residues: 1012 sheet: 0.59 (0.38), residues: 180 loop : -0.57 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 665 TYR 0.017 0.001 TYR D 377 PHE 0.014 0.001 PHE A 407 TRP 0.010 0.001 TRP C 239 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (18172) covalent geometry : angle 0.62296 / 0.30 (24696) SS BOND : bond 0.00506 / 0.24 ( 6) SS BOND : angle 0.74116 / 0.44 ( 12) hydrogen bonds : bond 0.03703 / 2.37 ( 735) hydrogen bonds : angle 4.21131 / 2.96 ( 2082) link_BETA1-4 : bond 0.00935 / 0.44 ( 10) link_BETA1-4 : angle 3.08799 / 1.95 ( 30) link_NAG-ASN : bond 0.00925 / 0.43 ( 10) link_NAG-ASN : angle 3.68923 / 2.40 ( 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: 53 poor density : 194 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8418 (t0) REVERT: A 512 ASP cc_start: 0.7671 (p0) cc_final: 0.7141 (p0) REVERT: A 610 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8289 (mmt) REVERT: A 653 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8084 (mtpt) REVERT: B 134 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 180 PHE cc_start: 0.5587 (m-10) cc_final: 0.5194 (m-10) REVERT: B 199 LEU cc_start: 0.7098 (tp) cc_final: 0.6863 (mt) REVERT: B 254 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.3511 (tp) REVERT: B 278 MET cc_start: 0.7089 (mtm) cc_final: 0.6883 (ttm) REVERT: B 323 THR cc_start: 0.5540 (OUTLIER) cc_final: 0.5191 (p) REVERT: B 365 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7492 (m-10) REVERT: B 402 GLU cc_start: 0.6036 (mp0) cc_final: 0.4092 (tp30) REVERT: C 271 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8409 (t0) REVERT: C 512 ASP cc_start: 0.7666 (p0) cc_final: 0.7297 (p0) REVERT: C 542 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8849 (mtpt) REVERT: C 610 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8276 (mmt) REVERT: C 653 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8090 (mtpt) REVERT: D 85 GLU cc_start: 0.5720 (tt0) cc_final: 0.5380 (tm-30) REVERT: D 107 ILE cc_start: 0.5459 (mt) cc_final: 0.5018 (pp) REVERT: D 134 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: D 180 PHE cc_start: 0.5707 (m-10) cc_final: 0.5391 (m-10) REVERT: D 199 LEU cc_start: 0.6960 (tp) cc_final: 0.6724 (mt) REVERT: D 263 VAL cc_start: 0.6269 (OUTLIER) cc_final: 0.5854 (p) REVERT: D 323 THR cc_start: 0.5439 (OUTLIER) cc_final: 0.5068 (p) REVERT: D 442 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6151 (mt) REVERT: D 471 MET cc_start: 0.7613 (mtm) cc_final: 0.7224 (mtt) outliers start: 53 outliers final: 22 residues processed: 233 average time/residue: 0.5196 time to fit residues: 137.2014 Evaluate side-chains 223 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 419 VAL 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 388 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 480 VAL 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 419 VAL 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 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 298 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4011 r_free = 0.4011 target = 0.178095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110611 restraints weight = 19271.604| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.79 r_work: 0.2877 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18198 Z= 0.164 Angle : 0.690 10.281 24768 Z= 0.333 Chirality : 0.049 0.315 2818 Planarity : 0.005 0.055 3056 Dihedral : 7.029 59.590 2492 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.70 % Allowed : 14.90 % Favored : 82.40 % 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: 0.11 (0.18), residues: 2154 helix: 0.75 (0.17), residues: 1004 sheet: 0.54 (0.38), residues: 180 loop : -0.68 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 665 TYR 0.019 0.002 TYR C 259 PHE 0.021 0.002 PHE C 407 TRP 0.014 0.002 TRP C 239 HIS 0.007 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (18172) covalent geometry : angle 0.66864 / 0.33 (24696) SS BOND : bond 0.00744 / 0.35 ( 6) SS BOND : angle 1.04987 / 0.62 ( 12) hydrogen bonds : bond 0.04392 / 2.80 ( 735) hydrogen bonds : angle 4.34049 / 3.05 ( 2082) link_BETA1-4 : bond 0.00909 / 0.44 ( 10) link_BETA1-4 : angle 3.17020 / 1.98 ( 30) link_NAG-ASN : bond 0.00869 / 0.40 ( 10) link_NAG-ASN : angle 3.84624 / 2.46 ( 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 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8479 (t0) REVERT: A 512 ASP cc_start: 0.7892 (p0) cc_final: 0.7380 (p0) REVERT: A 610 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8325 (mmt) REVERT: A 653 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8108 (mtpt) REVERT: B 134 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: B 199 LEU cc_start: 0.7073 (tp) cc_final: 0.6743 (mt) REVERT: B 254 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.3865 (tp) REVERT: B 278 MET cc_start: 0.7120 (mtm) cc_final: 0.6860 (ttm) REVERT: B 365 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: B 393 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3552 (tp) REVERT: B 402 GLU cc_start: 0.5926 (mp0) cc_final: 0.3941 (tp30) REVERT: B 442 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6213 (mt) REVERT: C 271 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8488 (t0) REVERT: C 512 ASP cc_start: 0.7881 (p0) cc_final: 0.7396 (p0) REVERT: C 542 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8875 (mtpt) REVERT: C 610 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8347 (mmt) REVERT: C 653 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8092 (mtpt) REVERT: D 85 GLU cc_start: 0.5589 (tt0) cc_final: 0.5249 (tm-30) REVERT: D 107 ILE cc_start: 0.5516 (mt) cc_final: 0.5049 (pp) REVERT: D 134 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: D 180 PHE cc_start: 0.5636 (m-10) cc_final: 0.5366 (m-10) REVERT: D 199 LEU cc_start: 0.6953 (tp) cc_final: 0.6688 (mt) REVERT: D 263 VAL cc_start: 0.6284 (OUTLIER) cc_final: 0.5866 (p) REVERT: D 323 THR cc_start: 0.5500 (OUTLIER) cc_final: 0.5158 (p) REVERT: D 442 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6147 (mt) REVERT: D 464 LYS cc_start: 0.4237 (OUTLIER) cc_final: 0.3777 (mmtp) REVERT: D 471 MET cc_start: 0.7607 (mtm) cc_final: 0.7190 (mtt) outliers start: 51 outliers final: 19 residues processed: 233 average time/residue: 0.5245 time to fit residues: 138.6179 Evaluate side-chains 223 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL 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 270 MET 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 403 LEU 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 419 VAL 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 276 THR 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: 20.0000 chunk 121 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4027 r_free = 0.4027 target = 0.179484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111533 restraints weight = 19311.183| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.87 r_work: 0.2940 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18198 Z= 0.124 Angle : 0.652 10.938 24768 Z= 0.312 Chirality : 0.047 0.293 2818 Planarity : 0.004 0.054 3056 Dihedral : 6.887 59.821 2492 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 15.43 % 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: 0.24 (0.18), residues: 2154 helix: 0.82 (0.17), residues: 1012 sheet: 0.58 (0.38), residues: 180 loop : -0.57 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 665 TYR 0.017 0.001 TYR D 377 PHE 0.016 0.001 PHE B 459 TRP 0.012 0.001 TRP A 239 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18172) covalent geometry : angle 0.62944 / 0.31 (24696) SS BOND : bond 0.00632 / 0.29 ( 6) SS BOND : angle 2.34218 / 1.42 ( 12) hydrogen bonds : bond 0.03745 / 2.39 ( 735) hydrogen bonds : angle 4.23322 / 2.98 ( 2082) link_BETA1-4 : bond 0.00947 / 0.46 ( 10) link_BETA1-4 : angle 3.05746 / 1.92 ( 30) link_NAG-ASN : bond 0.00888 / 0.41 ( 10) link_NAG-ASN : angle 3.57960 / 2.31 ( 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 226 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8456 (t0) REVERT: A 512 ASP cc_start: 0.7745 (p0) cc_final: 0.7183 (p0) REVERT: A 610 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8262 (mmt) REVERT: A 653 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8122 (mtpt) REVERT: B 134 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: B 180 PHE cc_start: 0.5805 (m-80) cc_final: 0.5536 (m-10) REVERT: B 199 LEU cc_start: 0.7043 (tp) cc_final: 0.6732 (mt) REVERT: B 254 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.3536 (tp) REVERT: B 278 MET cc_start: 0.6987 (mtm) cc_final: 0.6773 (ttm) REVERT: B 365 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: B 402 GLU cc_start: 0.5921 (mp0) cc_final: 0.3932 (tp30) REVERT: B 442 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6213 (mt) REVERT: B 467 LYS cc_start: 0.6705 (mttm) cc_final: 0.6322 (mmmt) REVERT: C 271 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8470 (t0) REVERT: C 512 ASP cc_start: 0.7738 (p0) cc_final: 0.7199 (p0) REVERT: C 610 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8260 (mmt) REVERT: C 653 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8109 (mtpt) REVERT: D 85 GLU cc_start: 0.5555 (tt0) cc_final: 0.5324 (tm-30) REVERT: D 107 ILE cc_start: 0.5470 (mt) cc_final: 0.5026 (pp) REVERT: D 134 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: D 180 PHE cc_start: 0.5696 (m-10) cc_final: 0.5471 (m-10) REVERT: D 199 LEU cc_start: 0.6906 (tp) cc_final: 0.6644 (mt) REVERT: D 263 VAL cc_start: 0.6333 (OUTLIER) cc_final: 0.5926 (p) REVERT: D 323 THR cc_start: 0.5505 (OUTLIER) cc_final: 0.5227 (p) REVERT: D 442 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6121 (mt) REVERT: D 464 LYS cc_start: 0.4242 (OUTLIER) cc_final: 0.3823 (mmtp) REVERT: D 471 MET cc_start: 0.7595 (mtm) cc_final: 0.7221 (mtt) outliers start: 44 outliers final: 16 residues processed: 215 average time/residue: 0.5248 time to fit residues: 127.1147 Evaluate side-chains 211 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 419 VAL 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 270 MET Chi-restraints excluded: chain B residue 279 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 419 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4036 r_free = 0.4036 target = 0.180258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113836 restraints weight = 19307.891| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.88 r_work: 0.2925 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18198 Z= 0.112 Angle : 0.637 10.217 24768 Z= 0.303 Chirality : 0.046 0.292 2818 Planarity : 0.004 0.053 3056 Dihedral : 6.736 58.630 2492 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.11 % Allowed : 15.75 % Favored : 82.14 % 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: 0.37 (0.18), residues: 2154 helix: 0.96 (0.17), residues: 1008 sheet: 0.59 (0.38), residues: 180 loop : -0.52 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 397 TYR 0.019 0.001 TYR D 377 PHE 0.017 0.001 PHE D 459 TRP 0.011 0.001 TRP C 569 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (18172) covalent geometry : angle 0.61664 / 0.30 (24696) SS BOND : bond 0.00500 / 0.23 ( 6) SS BOND : angle 1.64066 / 1.00 ( 12) hydrogen bonds : bond 0.03470 / 2.21 ( 735) hydrogen bonds : angle 4.16330 / 2.93 ( 2082) link_BETA1-4 : bond 0.00904 / 0.44 ( 10) link_BETA1-4 : angle 2.92719 / 1.84 ( 30) link_NAG-ASN : bond 0.00876 / 0.40 ( 10) link_NAG-ASN : angle 3.46559 / 2.24 ( 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 225 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8404 (t0) REVERT: A 432 MET cc_start: 0.9527 (mmm) cc_final: 0.9268 (mmp) REVERT: A 437 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: A 512 ASP cc_start: 0.7719 (p0) cc_final: 0.7426 (p0) REVERT: A 610 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (mmt) REVERT: A 653 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8091 (mtpt) REVERT: B 134 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: B 180 PHE cc_start: 0.5772 (m-10) cc_final: 0.5487 (m-10) REVERT: B 199 LEU cc_start: 0.7098 (tp) cc_final: 0.6812 (mt) REVERT: B 254 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.3482 (tp) REVERT: B 365 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: B 402 GLU cc_start: 0.5872 (mp0) cc_final: 0.3856 (tp30) REVERT: B 442 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6218 (mt) REVERT: B 467 LYS cc_start: 0.6732 (mttm) cc_final: 0.6321 (tppt) REVERT: C 271 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8406 (t0) REVERT: C 432 MET cc_start: 0.9536 (mmm) cc_final: 0.9273 (mmp) REVERT: C 512 ASP cc_start: 0.7708 (p0) cc_final: 0.7409 (p0) REVERT: C 610 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8254 (mmt) REVERT: C 653 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8064 (mtpt) REVERT: D 85 GLU cc_start: 0.5491 (tt0) cc_final: 0.5289 (tm-30) REVERT: D 107 ILE cc_start: 0.5505 (mt) cc_final: 0.5076 (pp) REVERT: D 134 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: D 180 PHE cc_start: 0.5766 (m-10) cc_final: 0.5538 (m-10) REVERT: D 199 LEU cc_start: 0.6889 (tp) cc_final: 0.6630 (mt) REVERT: D 263 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.5932 (p) REVERT: D 323 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.5277 (p) REVERT: D 442 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6196 (mt) REVERT: D 464 LYS cc_start: 0.4258 (OUTLIER) cc_final: 0.3888 (mmtp) REVERT: D 471 MET cc_start: 0.7609 (mtm) cc_final: 0.7225 (mtt) outliers start: 40 outliers final: 14 residues processed: 210 average time/residue: 0.5674 time to fit residues: 134.2131 Evaluate side-chains 213 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 419 VAL 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 270 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 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 419 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 276 THR 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: 5.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4019 r_free = 0.4019 target = 0.178857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108362 restraints weight = 19279.983| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.71 r_work: 0.2945 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18198 Z= 0.138 Angle : 0.666 10.521 24768 Z= 0.318 Chirality : 0.048 0.296 2818 Planarity : 0.004 0.051 3056 Dihedral : 6.914 59.982 2492 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.80 % Allowed : 16.07 % Favored : 82.14 % 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: 0.35 (0.18), residues: 2154 helix: 0.96 (0.17), residues: 1004 sheet: 0.55 (0.38), residues: 180 loop : -0.53 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 665 TYR 0.020 0.001 TYR D 377 PHE 0.018 0.001 PHE A 407 TRP 0.013 0.001 TRP A 239 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18172) covalent geometry : angle 0.64533 / 0.31 (24696) SS BOND : bond 0.00690 / 0.32 ( 6) SS BOND : angle 1.75078 / 1.06 ( 12) hydrogen bonds : bond 0.03946 / 2.51 ( 735) hydrogen bonds : angle 4.23824 / 2.99 ( 2082) link_BETA1-4 : bond 0.00872 / 0.43 ( 10) link_BETA1-4 : angle 2.95379 / 1.84 ( 30) link_NAG-ASN : bond 0.00857 / 0.39 ( 10) link_NAG-ASN : angle 3.60098 / 2.30 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.30 seconds wall clock time: 110 minutes 33.34 seconds (6633.34 seconds total)