Starting phenix.real_space_refine on Fri Oct 23 18:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25ex_80068/10_2026/25ex_80068.cif Found real_map, /net/cci-nas-00/data/ceres_data/25ex_80068/10_2026/25ex_80068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25ex_80068/10_2026/25ex_80068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25ex_80068/10_2026/25ex_80068.map" model { file = "/net/cci-nas-00/data/ceres_data/25ex_80068/10_2026/25ex_80068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25ex_80068/10_2026/25ex_80068.cif" } resolution = 2.66 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= 0.004 sd= 0.216 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 K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6964 2.51 5 N 1696 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10617 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5270 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5380 Chain: "B" Number of atoms: 5279 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5369 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 4.43, per 1000 atoms: 0.42 Number of scatterers: 10617 At special positions: 0 Unit cell: (119.58, 89.4159, 106.653, 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) K 2 19.00 S 60 16.00 P 4 15.00 O 1891 8.00 N 1696 7.00 C 6964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 870.2 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 3 sheets defined 69.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.715A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 93 through 110 removed outlier: 3.577A pdb=" N GLY A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.872A pdb=" N ASN A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.735A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.570A pdb=" N GLU A 154 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 4.345A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 4.019A pdb=" N LYS A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.793A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.856A pdb=" N VAL A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.605A pdb=" N LEU A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.680A pdb=" N VAL A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.587A pdb=" N ILE A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 322 through 349 removed outlier: 4.929A pdb=" N TYR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.544A pdb=" N SER A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.588A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 440 removed outlier: 4.345A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 removed outlier: 3.706A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 3.994A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 537 removed outlier: 3.735A pdb=" N VAL A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.779A pdb=" N ILE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.655A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 727 removed outlier: 3.554A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.532A pdb=" N LYS A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.614A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 56 through 70 removed outlier: 3.716A pdb=" N LEU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 93 through 110 removed outlier: 3.578A pdb=" N GLY B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.871A pdb=" N ASN B 122 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.532A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.562A pdb=" N GLU B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.810A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 4.010A pdb=" N LYS B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.798A pdb=" N SER B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.860A pdb=" N VAL B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.606A pdb=" N LEU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.699A pdb=" N VAL B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.588A pdb=" N ILE B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 322 through 349 removed outlier: 4.931A pdb=" N TYR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Proline residue: B 336 - end of helix Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.541A pdb=" N SER B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.585A pdb=" N THR B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 removed outlier: 4.344A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 472 removed outlier: 3.720A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 500 removed outlier: 3.989A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 537 removed outlier: 3.715A pdb=" N VAL B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.762A pdb=" N ILE B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 removed outlier: 4.347A pdb=" N SER B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.651A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 removed outlier: 3.577A pdb=" N LYS B 726 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.542A pdb=" N LYS B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.624A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 611 removed outlier: 7.628A pdb=" N PHE A 620 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 588 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N CYS A 622 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 590 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL A 624 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 592 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR A 626 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 594 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER A 583 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 556 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS A 585 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 558 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 729 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 559 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU A 731 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 561 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLY A 733 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N TYR A 563 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N THR A 735 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 777 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR A 783 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 785 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR A 738 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LEU B 777 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR B 730 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL B 779 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET B 732 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N MET B 781 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU B 734 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR B 783 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU B 736 " --> pdb=" O TYR B 783 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU B 785 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR B 738 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 729 " --> pdb=" O PRO B 557 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 559 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 731 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 561 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLY B 733 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N TYR B 563 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N THR B 735 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B 583 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 556 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS B 585 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 558 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE B 620 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 411 556 hydrogen bonds defined for protein. 1594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1604 1.30 - 1.43: 2946 1.43 - 1.55: 6195 1.55 - 1.68: 8 1.68 - 1.81: 104 Bond restraints: 10857 Sorted by residual: bond pdb=" C GLY A 627 " pdb=" O GLY A 627 " ideal model delta sigma weight residual 1.228 1.175 0.054 1.20e-02 6.94e+03 2.02e+01 bond pdb=" CA LYS A 629 " pdb=" C LYS A 629 " ideal model delta sigma weight residual 1.524 1.467 0.058 1.29e-02 6.01e+03 2.01e+01 bond pdb=" C GLY B 128 " pdb=" O GLY B 128 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.10e-02 8.26e+03 1.73e+01 bond pdb=" C GLY B 125 " pdb=" O GLY B 125 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.37e-02 5.33e+03 1.60e+01 bond pdb=" C GLY A 125 " pdb=" O GLY A 125 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.37e-02 5.33e+03 1.59e+01 ... (remaining 10852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14196 1.64 - 3.28: 430 3.28 - 4.92: 78 4.92 - 6.57: 34 6.57 - 8.21: 11 Bond angle restraints: 14749 Sorted by residual: angle pdb=" N ILE A 203 " pdb=" CA ILE A 203 " pdb=" C ILE A 203 " ideal model delta sigma weight residual 111.90 108.09 3.81 8.10e-01 1.52e+00 2.22e+01 angle pdb=" N LYS A 629 " pdb=" CA LYS A 629 " pdb=" C LYS A 629 " ideal model delta sigma weight residual 112.41 106.35 6.06 1.30e+00 5.92e-01 2.17e+01 angle pdb=" N ILE B 203 " pdb=" CA ILE B 203 " pdb=" C ILE B 203 " ideal model delta sigma weight residual 111.90 108.17 3.73 8.10e-01 1.52e+00 2.12e+01 angle pdb=" O ILE B 472 " pdb=" C ILE B 472 " pdb=" N TRP B 473 " ideal model delta sigma weight residual 122.23 117.76 4.47 9.80e-01 1.04e+00 2.08e+01 angle pdb=" CA GLY A 627 " pdb=" C GLY A 627 " pdb=" N TYR A 628 " ideal model delta sigma weight residual 114.55 119.67 -5.12 1.16e+00 7.43e-01 1.94e+01 ... (remaining 14744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.81: 5941 25.81 - 51.63: 372 51.63 - 77.44: 37 77.44 - 103.25: 7 103.25 - 129.07: 2 Dihedral angle restraints: 6359 sinusoidal: 2470 harmonic: 3889 Sorted by residual: dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 69.06 -129.07 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 53.33 -113.32 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" CA VAL A 457 " pdb=" C VAL A 457 " pdb=" N MET A 458 " pdb=" CA MET A 458 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 6356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1663 0.102 - 0.205: 61 0.205 - 0.307: 3 0.307 - 0.410: 0 0.410 - 0.512: 2 Chirality restraints: 1729 Sorted by residual: chirality pdb=" CA LYS B 474 " pdb=" N LYS B 474 " pdb=" C LYS B 474 " pdb=" CB LYS B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA LYS A 474 " pdb=" N LYS A 474 " pdb=" C LYS A 474 " pdb=" CB LYS A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA GLU A 534 " pdb=" N GLU A 534 " pdb=" C GLU A 534 " pdb=" CB GLU A 534 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1726 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 472 " -0.015 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C ILE A 472 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 472 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP A 473 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 472 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C ILE B 472 " -0.048 2.00e-02 2.50e+03 pdb=" O ILE B 472 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP B 473 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 443 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C THR B 443 " 0.035 2.00e-02 2.50e+03 pdb=" O THR B 443 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU B 444 " -0.012 2.00e-02 2.50e+03 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 3031 2.80 - 3.38: 11003 3.38 - 3.97: 20410 3.97 - 4.55: 30326 4.55 - 5.14: 43650 Nonbonded interactions: 108420 Sorted by model distance: nonbonded pdb=" OD1 ASP A 274 " pdb=" OG1 THR A 276 " model vdw 2.214 3.040 nonbonded pdb=" OH ATYR B 139 " pdb=" O ALA B 170 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP B 274 " pdb=" OG1 THR B 276 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP A 123 " pdb=" OH TYR A 628 " model vdw 2.276 3.040 nonbonded pdb=" O TYR B 289 " pdb=" OG1 THR B 293 " model vdw 2.276 3.040 ... (remaining 108415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 55 through 138 or resid 140 through 529 or resid 531 throu \ gh 902)) selection = (chain 'B' and (resid 55 through 138 or resid 140 through 529 or resid 531 throu \ gh 902)) } 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=0.50 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: 1.500 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.005 0.058 10857 Z= 0.295 Angle : 0.747 8.208 14749 Z= 0.430 Chirality : 0.049 0.512 1729 Planarity : 0.005 0.047 1788 Dihedral : 16.169 129.067 3873 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.46 % Favored : 93.31 % Rotamer: Outliers : 4.14 % Allowed : 17.00 % Favored : 78.86 % Cbeta Deviations : 0.24 % 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: -3.91 (0.19), residues: 1319 helix: -2.56 (0.14), residues: 839 sheet: -1.09 (0.51), residues: 102 loop : -2.57 (0.26), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 606 TYR 0.013 0.002 TYR B 104 PHE 0.011 0.001 PHE A 373 TRP 0.012 0.002 TRP A 370 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.30 (10857) covalent geometry : angle 0.74694 / 0.43 (14749) hydrogen bonds : bond 0.18480 / 12.07 ( 556) hydrogen bonds : angle 7.40234 / 4.96 ( 1594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.386 Fit side-chains REVERT: A 59 MET cc_start: 0.7920 (mmt) cc_final: 0.7495 (mmt) REVERT: A 112 LEU cc_start: 0.8541 (tp) cc_final: 0.8158 (tp) REVERT: A 119 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 139 TYR cc_start: 0.8187 (t80) cc_final: 0.6561 (m-80) REVERT: A 175 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 291 ARG cc_start: 0.6965 (ttm170) cc_final: 0.6513 (mtp180) REVERT: A 295 ARG cc_start: 0.6669 (mmt180) cc_final: 0.4485 (ttt-90) REVERT: A 324 ARG cc_start: 0.7224 (mmt-90) cc_final: 0.6939 (tpp-160) REVERT: A 541 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7512 (mtp180) REVERT: B 59 MET cc_start: 0.7929 (mmt) cc_final: 0.7504 (mmt) REVERT: B 119 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 291 ARG cc_start: 0.7065 (ttm170) cc_final: 0.6629 (mtp180) REVERT: B 295 ARG cc_start: 0.6672 (mmt180) cc_final: 0.4506 (ttt-90) REVERT: B 324 ARG cc_start: 0.7230 (mmt-90) cc_final: 0.6947 (tpp-160) REVERT: B 534 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7319 (mt-10) REVERT: B 541 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7560 (mtp180) outliers start: 47 outliers final: 23 residues processed: 211 average time/residue: 0.5492 time to fit residues: 124.6814 Evaluate side-chains 174 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 635 PRO Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 737 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 90 ASN A 223 ASN A 273 HIS A 282 ASN A 385 GLN A 448 HIS A 524 GLN A 641 HIS A 716 GLN B 64 GLN B 90 ASN B 223 ASN B 273 HIS B 282 ASN B 385 GLN B 448 HIS B 524 GLN B 641 HIS B 716 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134872 restraints weight = 16073.610| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.99 r_work: 0.3363 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10857 Z= 0.125 Angle : 0.623 7.000 14749 Z= 0.326 Chirality : 0.043 0.161 1729 Planarity : 0.005 0.048 1788 Dihedral : 9.021 121.428 1519 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.54 % Allowed : 17.34 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.21 (0.21), residues: 1319 helix: -1.15 (0.16), residues: 855 sheet: -1.00 (0.50), residues: 106 loop : -1.94 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.013 0.001 TYR B 70 PHE 0.018 0.001 PHE A 130 TRP 0.009 0.001 TRP A 370 HIS 0.004 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (10857) covalent geometry : angle 0.62289 / 0.33 (14749) hydrogen bonds : bond 0.04383 / 2.91 ( 556) hydrogen bonds : angle 5.02259 / 3.35 ( 1594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.403 Fit side-chains REVERT: A 59 MET cc_start: 0.7950 (mmt) cc_final: 0.7634 (mmt) REVERT: A 112 LEU cc_start: 0.8871 (tp) cc_final: 0.8555 (tp) REVERT: A 120 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7045 (mp-120) REVERT: A 139 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: A 295 ARG cc_start: 0.6661 (mmt180) cc_final: 0.4296 (ttt-90) REVERT: A 324 ARG cc_start: 0.7686 (mmt-90) cc_final: 0.7479 (tpp-160) REVERT: A 430 MET cc_start: 0.8270 (ttp) cc_final: 0.7971 (ttm) REVERT: A 444 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7252 (tt0) REVERT: A 524 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8878 (tp40) REVERT: A 540 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 541 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7806 (mtp180) REVERT: A 581 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 59 MET cc_start: 0.7952 (mmt) cc_final: 0.7592 (mmt) REVERT: B 112 LEU cc_start: 0.8899 (tp) cc_final: 0.8561 (tp) REVERT: B 120 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6997 (mp-120) REVERT: B 295 ARG cc_start: 0.6653 (mmt180) cc_final: 0.4271 (ttt-90) REVERT: B 524 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8892 (tp40) REVERT: B 534 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8004 (mt-10) REVERT: B 541 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7778 (mtp180) outliers start: 40 outliers final: 17 residues processed: 188 average time/residue: 0.5899 time to fit residues: 118.6211 Evaluate side-chains 168 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [19, 126, 68, 55, 7, 91, 96, 107, 112, 95, 109] chunk 19 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134727 restraints weight = 25067.693| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.80 r_work: 0.3340 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10857 Z= 0.139 Angle : 0.624 7.298 14749 Z= 0.325 Chirality : 0.043 0.196 1729 Planarity : 0.004 0.048 1788 Dihedral : 8.459 121.310 1493 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.06 % Allowed : 17.34 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.57 (0.22), residues: 1319 helix: -0.67 (0.17), residues: 859 sheet: -0.79 (0.49), residues: 108 loop : -1.66 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.013 0.002 TYR B 427 PHE 0.025 0.001 PHE B 502 TRP 0.012 0.002 TRP B 523 HIS 0.005 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10857) covalent geometry : angle 0.62391 / 0.32 (14749) hydrogen bonds : bond 0.04547 / 3.03 ( 556) hydrogen bonds : angle 4.88894 / 3.25 ( 1594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.391 Fit side-chains REVERT: A 59 MET cc_start: 0.8000 (mmt) cc_final: 0.7706 (mmt) REVERT: A 120 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6829 (mp-120) REVERT: A 139 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 295 ARG cc_start: 0.6495 (mmt180) cc_final: 0.4103 (ttt-90) REVERT: A 324 ARG cc_start: 0.7653 (mmt-90) cc_final: 0.7252 (tpp-160) REVERT: A 430 MET cc_start: 0.8177 (ttp) cc_final: 0.7828 (ttm) REVERT: A 444 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7124 (tt0) REVERT: A 524 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8855 (tp40) REVERT: A 534 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 540 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8137 (p) REVERT: A 541 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7718 (mtp180) REVERT: A 603 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7582 (m) REVERT: A 722 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7035 (tmmt) REVERT: A 724 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7212 (ttt-90) REVERT: B 59 MET cc_start: 0.7993 (mmt) cc_final: 0.7609 (mmt) REVERT: B 120 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.6840 (mp-120) REVERT: B 295 ARG cc_start: 0.6480 (mmt180) cc_final: 0.4082 (ttt-90) REVERT: B 534 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7925 (mt-10) REVERT: B 722 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7084 (tmmt) outliers start: 46 outliers final: 20 residues processed: 174 average time/residue: 0.6060 time to fit residues: 112.8989 Evaluate side-chains 169 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 722 LYS Chi-restraints excluded: chain B residue 737 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [64, 53, 86, 99, 49, 22, 107, 90, 2, 47, 106] chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137236 restraints weight = 23063.835| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.47 r_work: 0.3382 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10857 Z= 0.116 Angle : 0.590 7.061 14749 Z= 0.306 Chirality : 0.042 0.184 1729 Planarity : 0.004 0.050 1788 Dihedral : 8.159 119.265 1487 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.06 % Allowed : 16.65 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.02 (0.23), residues: 1319 helix: -0.27 (0.18), residues: 849 sheet: -0.47 (0.50), residues: 106 loop : -1.39 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.012 0.001 TYR A 70 PHE 0.027 0.001 PHE A 182 TRP 0.014 0.001 TRP A 523 HIS 0.004 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10857) covalent geometry : angle 0.59042 / 0.31 (14749) hydrogen bonds : bond 0.03930 / 2.61 ( 556) hydrogen bonds : angle 4.64578 / 3.09 ( 1594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.374 Fit side-chains REVERT: A 59 MET cc_start: 0.8013 (mmt) cc_final: 0.7767 (mmt) REVERT: A 120 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7042 (mp-120) REVERT: A 139 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: A 295 ARG cc_start: 0.6376 (mmt180) cc_final: 0.3928 (ttt-90) REVERT: A 324 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.7350 (tpp-160) REVERT: A 430 MET cc_start: 0.8222 (ttp) cc_final: 0.7888 (ttm) REVERT: A 524 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8868 (tp40) REVERT: A 534 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 722 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7052 (tmmt) REVERT: B 59 MET cc_start: 0.7980 (mmt) cc_final: 0.7665 (mmt) REVERT: B 116 PHE cc_start: 0.8366 (m-10) cc_final: 0.8093 (m-10) REVERT: B 120 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.6899 (mp-120) REVERT: B 295 ARG cc_start: 0.6362 (mmt180) cc_final: 0.3941 (ttt-90) REVERT: B 430 MET cc_start: 0.8220 (ttp) cc_final: 0.7914 (ttm) REVERT: B 524 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8899 (tp40) REVERT: B 534 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8072 (mt-10) REVERT: B 541 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7421 (mtp180) REVERT: B 603 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7413 (m) REVERT: B 610 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7894 (ttp-110) REVERT: B 722 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7080 (tmmt) outliers start: 46 outliers final: 19 residues processed: 191 average time/residue: 0.5800 time to fit residues: 118.8588 Evaluate side-chains 175 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 722 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [93, 22, 40, 57, 16, 44, 105, 110, 78, 113, 90] chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132881 restraints weight = 27721.372| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.20 r_work: 0.3327 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10857 Z= 0.161 Angle : 0.646 7.672 14749 Z= 0.335 Chirality : 0.044 0.181 1729 Planarity : 0.005 0.047 1788 Dihedral : 8.386 122.212 1487 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.45 % Allowed : 17.60 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.08 (0.23), residues: 1319 helix: -0.37 (0.18), residues: 863 sheet: -0.41 (0.50), residues: 108 loop : -1.33 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.016 0.002 TYR A 104 PHE 0.023 0.002 PHE B 502 TRP 0.011 0.001 TRP B 258 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10857) covalent geometry : angle 0.64582 / 0.34 (14749) hydrogen bonds : bond 0.04671 / 3.13 ( 556) hydrogen bonds : angle 4.82566 / 3.21 ( 1594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.382 Fit side-chains REVERT: A 59 MET cc_start: 0.8055 (mmt) cc_final: 0.7762 (mmt) REVERT: A 116 PHE cc_start: 0.8268 (m-10) cc_final: 0.7994 (m-10) REVERT: A 119 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 120 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6904 (mp-120) REVERT: A 139 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 295 ARG cc_start: 0.6344 (mmt180) cc_final: 0.3960 (ttt-90) REVERT: A 324 ARG cc_start: 0.7686 (mmt-90) cc_final: 0.7349 (tpp-160) REVERT: A 415 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7644 (mtmm) REVERT: A 430 MET cc_start: 0.8190 (ttp) cc_final: 0.7851 (ttm) REVERT: A 534 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 581 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8095 (mm) REVERT: A 603 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7454 (m) REVERT: A 722 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7143 (tmmt) REVERT: B 59 MET cc_start: 0.8050 (mmt) cc_final: 0.7692 (mmt) REVERT: B 116 PHE cc_start: 0.8272 (m-10) cc_final: 0.7999 (m-10) REVERT: B 119 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 120 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6878 (mp-120) REVERT: B 295 ARG cc_start: 0.6325 (mmt180) cc_final: 0.3963 (ttt-90) REVERT: B 415 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7694 (mtmm) REVERT: B 430 MET cc_start: 0.8219 (ttp) cc_final: 0.7883 (ttm) REVERT: B 541 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: B 603 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7451 (m) REVERT: B 722 LYS cc_start: 0.7736 (tppt) cc_final: 0.7184 (tmmt) outliers start: 39 outliers final: 20 residues processed: 176 average time/residue: 0.5718 time to fit residues: 108.2022 Evaluate side-chains 170 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 737 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [1, 34, 97, 77, 109, 86, 36, 104, 85, 33, 50] chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 chunk 36 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.164699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137779 restraints weight = 21132.718| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.15 r_work: 0.3443 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10857 Z= 0.105 Angle : 0.574 6.731 14749 Z= 0.296 Chirality : 0.042 0.181 1729 Planarity : 0.004 0.049 1788 Dihedral : 7.907 117.274 1487 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.45 % Allowed : 17.95 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.55 (0.24), residues: 1319 helix: 0.10 (0.18), residues: 843 sheet: -0.30 (0.51), residues: 106 loop : -1.21 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.012 0.001 TYR A 755 PHE 0.029 0.001 PHE B 182 TRP 0.011 0.001 TRP B 523 HIS 0.003 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10857) covalent geometry : angle 0.57360 / 0.30 (14749) hydrogen bonds : bond 0.03579 / 2.37 ( 556) hydrogen bonds : angle 4.49821 / 3.00 ( 1594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.383 Fit side-chains REVERT: A 59 MET cc_start: 0.7994 (mmt) cc_final: 0.7755 (mmt) REVERT: A 119 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 120 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7091 (mp-120) REVERT: A 139 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: A 295 ARG cc_start: 0.6060 (mmt180) cc_final: 0.3642 (ttt-90) REVERT: A 324 ARG cc_start: 0.7678 (mmt-90) cc_final: 0.7324 (tpp-160) REVERT: A 430 MET cc_start: 0.8238 (ttp) cc_final: 0.7888 (ttm) REVERT: A 534 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 640 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7138 (ttp80) REVERT: A 722 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6937 (tmmt) REVERT: B 59 MET cc_start: 0.8012 (mmt) cc_final: 0.7782 (mmt) REVERT: B 116 PHE cc_start: 0.8327 (m-10) cc_final: 0.8101 (m-10) REVERT: B 120 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7024 (mp-120) REVERT: B 295 ARG cc_start: 0.6043 (mmt180) cc_final: 0.3665 (ttt-90) REVERT: B 430 MET cc_start: 0.8270 (ttp) cc_final: 0.7974 (ttm) REVERT: B 534 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 542 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7459 (mp0) REVERT: B 722 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6976 (tmmt) outliers start: 39 outliers final: 16 residues processed: 180 average time/residue: 0.5779 time to fit residues: 111.7457 Evaluate side-chains 172 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 722 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [57, 11, 55, 26, 14, 17, 40, 100, 46, 87, 61] chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 100 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.4295 > 50:) chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132935 restraints weight = 28314.228| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.20 r_work: 0.3292 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10857 Z= 0.182 Angle : 0.665 7.766 14749 Z= 0.344 Chirality : 0.045 0.190 1729 Planarity : 0.005 0.045 1788 Dihedral : 8.233 123.756 1482 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.85 % Allowed : 19.41 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.90 (0.23), residues: 1319 helix: -0.24 (0.18), residues: 863 sheet: -0.31 (0.51), residues: 108 loop : -1.24 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 406 TYR 0.018 0.002 TYR B 104 PHE 0.024 0.002 PHE A 502 TRP 0.011 0.002 TRP B 258 HIS 0.007 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (10857) covalent geometry : angle 0.66540 / 0.34 (14749) hydrogen bonds : bond 0.04896 / 3.28 ( 556) hydrogen bonds : angle 4.88437 / 3.24 ( 1594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.388 Fit side-chains REVERT: A 59 MET cc_start: 0.8089 (mmt) cc_final: 0.7759 (mmt) REVERT: A 116 PHE cc_start: 0.8274 (m-10) cc_final: 0.8037 (m-10) REVERT: A 119 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 120 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6986 (mp-120) REVERT: A 139 TYR cc_start: 0.8194 (t80) cc_final: 0.6553 (m-80) REVERT: A 172 MET cc_start: 0.6776 (tmm) cc_final: 0.6539 (ttm) REVERT: A 295 ARG cc_start: 0.6095 (mmt180) cc_final: 0.3702 (ttt-90) REVERT: A 324 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7336 (tpp-160) REVERT: A 430 MET cc_start: 0.8142 (ttp) cc_final: 0.7785 (ttm) REVERT: A 524 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8835 (tp40) REVERT: A 534 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 603 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7420 (m) REVERT: A 640 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6812 (ttp80) REVERT: B 59 MET cc_start: 0.8097 (mmt) cc_final: 0.7741 (mmt) REVERT: B 116 PHE cc_start: 0.8283 (m-10) cc_final: 0.8050 (m-10) REVERT: B 120 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.6861 (mp-120) REVERT: B 295 ARG cc_start: 0.6084 (mmt180) cc_final: 0.3705 (ttt-90) REVERT: B 430 MET cc_start: 0.8175 (ttp) cc_final: 0.7856 (ttm) REVERT: B 524 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8893 (tp40) REVERT: B 542 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7466 (mp0) REVERT: B 640 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7168 (ttp80) outliers start: 32 outliers final: 17 residues processed: 165 average time/residue: 0.6056 time to fit residues: 107.1492 Evaluate side-chains 162 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 640 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 737 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [36, 84, 77, 105, 124, 117, 7, 23, 83, 131, 123] chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 chunk 123 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136904 restraints weight = 28489.695| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.13 r_work: 0.3348 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10857 Z= 0.112 Angle : 0.586 6.996 14749 Z= 0.303 Chirality : 0.042 0.190 1729 Planarity : 0.004 0.048 1788 Dihedral : 7.798 116.926 1480 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.59 % Allowed : 19.41 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.54 (0.23), residues: 1319 helix: 0.08 (0.18), residues: 849 sheet: -0.24 (0.51), residues: 106 loop : -1.17 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.012 0.001 TYR A 755 PHE 0.034 0.001 PHE B 182 TRP 0.008 0.001 TRP A 370 HIS 0.007 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10857) covalent geometry : angle 0.58615 / 0.30 (14749) hydrogen bonds : bond 0.03736 / 2.49 ( 556) hydrogen bonds : angle 4.57407 / 3.05 ( 1594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.411 Fit side-chains REVERT: A 59 MET cc_start: 0.8002 (mmt) cc_final: 0.7747 (mmt) REVERT: A 116 PHE cc_start: 0.8253 (m-10) cc_final: 0.8009 (m-10) REVERT: A 119 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 120 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7047 (mp-120) REVERT: A 139 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: A 324 ARG cc_start: 0.7634 (mmt-90) cc_final: 0.7284 (tpp-160) REVERT: A 430 MET cc_start: 0.8168 (ttp) cc_final: 0.7803 (ttm) REVERT: A 524 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8728 (tp40) REVERT: A 534 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 722 LYS cc_start: 0.7674 (tppt) cc_final: 0.7082 (tmmt) REVERT: B 59 MET cc_start: 0.7970 (mmt) cc_final: 0.7674 (mmt) REVERT: B 116 PHE cc_start: 0.8274 (m-10) cc_final: 0.8043 (m-10) REVERT: B 120 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7009 (mp-120) REVERT: B 430 MET cc_start: 0.8179 (ttp) cc_final: 0.7839 (ttm) REVERT: B 542 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7490 (mp0) REVERT: B 603 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7367 (m) REVERT: B 640 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7151 (ptp90) outliers start: 29 outliers final: 18 residues processed: 163 average time/residue: 0.5631 time to fit residues: 98.7786 Evaluate side-chains 162 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 744 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [51, 10, 61, 0, 114, 102, 30, 105, 41, 40, 18] chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136489 restraints weight = 24279.904| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.61 r_work: 0.3426 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10857 Z= 0.106 Angle : 0.578 6.824 14749 Z= 0.298 Chirality : 0.042 0.200 1729 Planarity : 0.004 0.043 1788 Dihedral : 7.582 115.991 1480 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.33 % Allowed : 20.19 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1319 helix: 0.27 (0.18), residues: 849 sheet: -0.34 (0.51), residues: 108 loop : -1.08 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 241 TYR 0.012 0.001 TYR A 755 PHE 0.024 0.001 PHE B 502 TRP 0.011 0.001 TRP B 523 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (10857) covalent geometry : angle 0.57769 / 0.30 (14749) hydrogen bonds : bond 0.03556 / 2.36 ( 556) hydrogen bonds : angle 4.45445 / 2.97 ( 1594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.380 Fit side-chains REVERT: A 59 MET cc_start: 0.7981 (mmt) cc_final: 0.7757 (mmt) REVERT: A 116 PHE cc_start: 0.8362 (m-10) cc_final: 0.8116 (m-10) REVERT: A 119 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 120 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7090 (mp-120) REVERT: A 139 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: A 172 MET cc_start: 0.6446 (ttm) cc_final: 0.5454 (mmt) REVERT: A 324 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.7370 (tpp-160) REVERT: A 430 MET cc_start: 0.8250 (ttp) cc_final: 0.7919 (ttm) REVERT: A 493 LEU cc_start: 0.8507 (tp) cc_final: 0.8304 (tp) REVERT: A 524 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8688 (tp40) REVERT: A 534 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 640 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7105 (ttp80) REVERT: A 722 LYS cc_start: 0.7572 (tppt) cc_final: 0.6967 (tmmt) REVERT: B 59 MET cc_start: 0.8001 (mmt) cc_final: 0.7774 (mmt) REVERT: B 112 LEU cc_start: 0.8762 (tp) cc_final: 0.8546 (tm) REVERT: B 116 PHE cc_start: 0.8385 (m-10) cc_final: 0.8133 (m-10) REVERT: B 120 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7120 (mp-120) REVERT: B 172 MET cc_start: 0.6385 (mmp) cc_final: 0.5809 (tmm) REVERT: B 430 MET cc_start: 0.8226 (ttp) cc_final: 0.7905 (ttm) REVERT: B 542 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7505 (mp0) REVERT: B 603 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7367 (m) REVERT: B 640 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7236 (ptp90) outliers start: 26 outliers final: 13 residues processed: 164 average time/residue: 0.5684 time to fit residues: 100.3868 Evaluate side-chains 162 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 744 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [5, 65, 13, 67, 108, 70, 117, 51, 104, 115, 97] chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 0.0030 chunk 97 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137422 restraints weight = 28710.696| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.29 r_work: 0.3381 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10857 Z= 0.110 Angle : 0.582 6.875 14749 Z= 0.300 Chirality : 0.042 0.200 1729 Planarity : 0.004 0.046 1788 Dihedral : 7.523 116.573 1479 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.16 % Allowed : 20.53 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.28 (0.24), residues: 1319 helix: 0.33 (0.18), residues: 847 sheet: -0.20 (0.52), residues: 106 loop : -1.16 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 241 TYR 0.012 0.001 TYR A 755 PHE 0.038 0.001 PHE A 182 TRP 0.009 0.001 TRP B 523 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10857) covalent geometry : angle 0.58185 / 0.30 (14749) hydrogen bonds : bond 0.03595 / 2.39 ( 556) hydrogen bonds : angle 4.44786 / 2.97 ( 1594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.380 Fit side-chains REVERT: A 59 MET cc_start: 0.7908 (mmt) cc_final: 0.7698 (mmt) REVERT: A 112 LEU cc_start: 0.8760 (tp) cc_final: 0.8549 (tm) REVERT: A 116 PHE cc_start: 0.8259 (m-10) cc_final: 0.8015 (m-10) REVERT: A 119 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 120 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6998 (mp-120) REVERT: A 139 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: A 172 MET cc_start: 0.6421 (ttm) cc_final: 0.5445 (mmt) REVERT: A 324 ARG cc_start: 0.7612 (mmt-90) cc_final: 0.7267 (tpp-160) REVERT: A 430 MET cc_start: 0.8198 (ttp) cc_final: 0.7854 (ttm) REVERT: A 493 LEU cc_start: 0.8465 (tp) cc_final: 0.8263 (tp) REVERT: A 534 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 640 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7137 (ptp90) REVERT: A 722 LYS cc_start: 0.7528 (tppt) cc_final: 0.6928 (tmmt) REVERT: A 744 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 59 MET cc_start: 0.7903 (mmt) cc_final: 0.7639 (mmt) REVERT: B 112 LEU cc_start: 0.8736 (tp) cc_final: 0.8527 (tm) REVERT: B 116 PHE cc_start: 0.8284 (m-10) cc_final: 0.8038 (m-10) REVERT: B 119 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7876 (mp) REVERT: B 120 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7013 (mp-120) REVERT: B 172 MET cc_start: 0.6373 (mmp) cc_final: 0.5837 (tmm) REVERT: B 430 MET cc_start: 0.8180 (ttp) cc_final: 0.7848 (ttm) REVERT: B 542 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7418 (mp0) REVERT: B 603 SER cc_start: 0.7708 (OUTLIER) cc_final: 0.7391 (m) REVERT: B 640 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7159 (ptp90) REVERT: B 722 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6945 (tmmt) outliers start: 24 outliers final: 11 residues processed: 158 average time/residue: 0.5879 time to fit residues: 99.8720 Evaluate side-chains 164 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 722 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [123, 71, 101, 38, 8, 60, 89, 20, 39, 124, 51] chunk 123 optimal weight: 0.0000 chunk 71 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 51 optimal weight: 0.0170 overall best weight: 0.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136586 restraints weight = 26551.401| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.20 r_work: 0.3347 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10857 Z= 0.098 Angle : 0.558 6.796 14749 Z= 0.287 Chirality : 0.042 0.196 1729 Planarity : 0.004 0.045 1788 Dihedral : 7.222 115.178 1479 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.81 % Allowed : 20.62 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.15 (0.24), residues: 1319 helix: 0.64 (0.19), residues: 835 sheet: -0.12 (0.53), residues: 106 loop : -0.85 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.011 0.001 TYR A 755 PHE 0.023 0.001 PHE B 502 TRP 0.013 0.001 TRP A 523 HIS 0.002 0.000 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (10857) covalent geometry : angle 0.55827 / 0.29 (14749) hydrogen bonds : bond 0.03141 / 2.07 ( 556) hydrogen bonds : angle 4.27623 / 2.86 ( 1594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.64 seconds wall clock time: 66 minutes 40.38 seconds (4000.38 seconds total)