Starting phenix.real_space_refine on Sat Oct 11 10:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4s_42976/10_2025/8v4s_42976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4s_42976/10_2025/8v4s_42976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v4s_42976/10_2025/8v4s_42976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4s_42976/10_2025/8v4s_42976.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4s_42976/10_2025/8v4s_42976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4s_42976/10_2025/8v4s_42976.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 Zn 6 6.06 5 P 6 5.49 5 S 108 5.16 5 C 8748 2.51 5 N 2268 2.21 5 O 2721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13857 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4420 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 94 Unusual residues: {' ZN': 2, 'NAG': 3, 'PLM': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3490 SG CYS A 479 66.138 70.496 13.932 1.00 96.45 S ATOM 3643 SG CYS A 499 65.615 67.427 16.060 1.00 84.81 S ATOM 3700 SG CYS A 506 64.148 67.599 12.516 1.00 86.54 S ATOM 4221 SG CYS A 572 62.626 69.612 15.321 1.00 76.35 S ATOM 3475 SG CYS A 477 67.391 73.937 14.587 1.00 93.73 S ATOM 3490 SG CYS A 479 66.138 70.496 13.932 1.00 96.45 S ATOM 3508 SG CYS A 482 64.089 72.928 16.085 1.00 85.78 S ATOM 3637 SG CYS A 498 67.221 71.311 17.475 1.00 81.54 S Restraints were copied for chains: B, C Time building chain proxies: 4.31, per 1000 atoms: 0.31 Number of scatterers: 13857 At special positions: 0 Unit cell: (90.072, 95.256, 160.704, 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) Zn 6 29.99 S 108 16.00 P 6 15.00 O 2721 8.00 N 2268 7.00 C 8748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.04 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=15, symmetry=0 Links applied NAG-ASN " NAG A 604 " - " ASN A 202 " " NAG A 605 " - " ASN A 187 " " NAG A 606 " - " ASN A 241 " " NAG B 604 " - " ASN B 202 " " NAG B 605 " - " ASN B 187 " " NAG B 606 " - " ASN B 241 " " NAG C 604 " - " ASN C 202 " " NAG C 605 " - " ASN C 187 " " NAG C 606 " - " ASN C 241 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 621.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 499 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 506 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 479 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 479 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 482 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 477 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 498 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 499 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 506 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 572 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 479 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 479 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 482 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 477 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 498 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 499 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 506 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 572 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 479 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 479 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 482 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 477 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 498 " Number of angles added : 36 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 24 sheets defined 37.4% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.582A pdb=" N THR A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.835A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.940A pdb=" N VAL A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.853A pdb=" N HIS A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.774A pdb=" N PHE A 288 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 removed outlier: 4.594A pdb=" N SER A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 360 through 366 removed outlier: 4.426A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.915A pdb=" N SER A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.114A pdb=" N ALA A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.897A pdb=" N SER A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 removed outlier: 3.707A pdb=" N GLN A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.583A pdb=" N THR B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.835A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.939A pdb=" N VAL B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.853A pdb=" N HIS B 267 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.774A pdb=" N PHE B 288 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 removed outlier: 4.596A pdb=" N SER B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 360 through 366 removed outlier: 4.426A pdb=" N ARG B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.915A pdb=" N SER B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 378 Proline residue: B 376 - end of helix Processing helix chain 'B' and resid 379 through 387 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 488 through 493 removed outlier: 4.115A pdb=" N ALA B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 506 through 509 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.898A pdb=" N SER B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 removed outlier: 3.707A pdb=" N GLN B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 23 through 49 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.582A pdb=" N THR C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 231 through 238 removed outlier: 3.835A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.940A pdb=" N VAL C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.853A pdb=" N HIS C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.773A pdb=" N PHE C 288 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 342 removed outlier: 4.595A pdb=" N SER C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.427A pdb=" N ARG C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.916A pdb=" N SER C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 378 Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 379 through 387 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.114A pdb=" N ALA C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.898A pdb=" N SER C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 removed outlier: 3.707A pdb=" N GLN C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 558 Processing helix chain 'C' and resid 560 through 565 Processing helix chain 'C' and resid 570 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.874A pdb=" N VAL A 18 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 391 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG A 20 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 111 removed outlier: 6.729A pdb=" N PHE A 313 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR A 108 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 311 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A 110 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 309 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 120 removed outlier: 7.088A pdb=" N THR A 161 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG A 151 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLU A 163 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP A 139 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY A 150 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS A 137 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 398 through 401 Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AB3, first strand: chain 'B' and resid 101 through 111 removed outlier: 6.729A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS B 311 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS B 110 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 309 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 115 through 120 removed outlier: 7.088A pdb=" N THR B 161 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG B 151 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU B 163 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP B 139 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY B 150 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 137 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 398 through 401 Processing sheet with id=AB9, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AC1, first strand: chain 'C' and resid 101 through 111 removed outlier: 6.729A pdb=" N PHE C 313 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR C 108 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 311 " --> pdb=" O TYR C 108 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS C 110 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU C 309 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AC4, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AC5, first strand: chain 'C' and resid 115 through 120 removed outlier: 7.088A pdb=" N THR C 161 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG C 151 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLU C 163 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP C 139 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY C 150 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS C 137 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 398 through 401 585 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4238 1.34 - 1.46: 3408 1.46 - 1.58: 6166 1.58 - 1.70: 12 1.70 - 1.82: 135 Bond restraints: 13959 Sorted by residual: bond pdb=" CA SER A 360 " pdb=" C SER A 360 " ideal model delta sigma weight residual 1.525 1.591 -0.067 1.32e-02 5.74e+03 2.54e+01 bond pdb=" CA SER C 360 " pdb=" C SER C 360 " ideal model delta sigma weight residual 1.525 1.591 -0.066 1.32e-02 5.74e+03 2.54e+01 bond pdb=" CA SER B 360 " pdb=" C SER B 360 " ideal model delta sigma weight residual 1.525 1.591 -0.066 1.32e-02 5.74e+03 2.50e+01 bond pdb=" N LEU B 118 " pdb=" CA LEU B 118 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.44e+00 bond pdb=" N LEU A 118 " pdb=" CA LEU A 118 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.35e+00 ... (remaining 13954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17982 1.38 - 2.75: 703 2.75 - 4.13: 143 4.13 - 5.50: 33 5.50 - 6.88: 15 Bond angle restraints: 18876 Sorted by residual: angle pdb=" CA CYS B 374 " pdb=" C CYS B 374 " pdb=" O CYS B 374 " ideal model delta sigma weight residual 119.28 124.06 -4.78 1.21e+00 6.83e-01 1.56e+01 angle pdb=" CA CYS C 374 " pdb=" C CYS C 374 " pdb=" O CYS C 374 " ideal model delta sigma weight residual 119.28 124.06 -4.78 1.21e+00 6.83e-01 1.56e+01 angle pdb=" CA CYS A 374 " pdb=" C CYS A 374 " pdb=" O CYS A 374 " ideal model delta sigma weight residual 119.28 124.05 -4.77 1.21e+00 6.83e-01 1.55e+01 angle pdb=" CA CYS A 362 " pdb=" C CYS A 362 " pdb=" O CYS A 362 " ideal model delta sigma weight residual 119.38 123.79 -4.41 1.23e+00 6.61e-01 1.28e+01 angle pdb=" CA CYS B 362 " pdb=" C CYS B 362 " pdb=" O CYS B 362 " ideal model delta sigma weight residual 119.38 123.78 -4.40 1.23e+00 6.61e-01 1.28e+01 ... (remaining 18871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 8010 24.08 - 48.16: 401 48.16 - 72.24: 67 72.24 - 96.32: 9 96.32 - 120.40: 3 Dihedral angle restraints: 8490 sinusoidal: 3639 harmonic: 4851 Sorted by residual: dihedral pdb=" CB CYS A 129 " pdb=" SG CYS A 129 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual -86.00 -141.37 55.37 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS B 129 " pdb=" SG CYS B 129 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual -86.00 -141.37 55.37 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS C 129 " pdb=" SG CYS C 129 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual -86.00 -141.34 55.34 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 8487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1349 0.039 - 0.077: 485 0.077 - 0.116: 165 0.116 - 0.154: 26 0.154 - 0.193: 6 Chirality restraints: 2031 Sorted by residual: chirality pdb=" CA SER A 360 " pdb=" N SER A 360 " pdb=" C SER A 360 " pdb=" CB SER A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA SER C 360 " pdb=" N SER C 360 " pdb=" C SER C 360 " pdb=" CB SER C 360 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA SER B 360 " pdb=" N SER B 360 " pdb=" C SER B 360 " pdb=" CB SER B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2028 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 551 " 0.236 9.50e-02 1.11e+02 1.06e-01 6.88e+00 pdb=" NE ARG C 551 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 551 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 551 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 551 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 551 " 0.236 9.50e-02 1.11e+02 1.06e-01 6.85e+00 pdb=" NE ARG B 551 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 551 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 551 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 551 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 551 " 0.236 9.50e-02 1.11e+02 1.06e-01 6.85e+00 pdb=" NE ARG A 551 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 551 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 551 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 551 " 0.008 2.00e-02 2.50e+03 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2856 2.78 - 3.31: 12167 3.31 - 3.84: 23428 3.84 - 4.37: 29384 4.37 - 4.90: 48535 Nonbonded interactions: 116370 Sorted by model distance: nonbonded pdb=" OH TYR B 26 " pdb=" OD1 ASN B 380 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A 26 " pdb=" OD1 ASN A 380 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR C 26 " pdb=" OD1 ASN C 380 " model vdw 2.253 3.040 nonbonded pdb=" NZ LYS A 300 " pdb=" OH TYR B 299 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR A 299 " pdb=" NZ LYS C 300 " model vdw 2.313 3.120 ... (remaining 116365 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 0.067 14022 Z= 0.280 Angle : 0.673 6.880 18969 Z= 0.386 Chirality : 0.045 0.193 2031 Planarity : 0.006 0.106 2370 Dihedral : 13.992 120.403 5331 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.42 % Allowed : 9.77 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.21), residues: 1638 helix: 0.73 (0.24), residues: 465 sheet: 0.25 (0.27), residues: 357 loop : 0.33 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 53 TYR 0.015 0.002 TYR B 550 PHE 0.011 0.002 PHE C 436 TRP 0.011 0.001 TRP B 575 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00461 (13959) covalent geometry : angle 0.66366 (18876) SS BOND : bond 0.00246 ( 15) SS BOND : angle 1.07516 ( 30) hydrogen bonds : bond 0.15198 ( 555) hydrogen bonds : angle 6.53059 ( 1584) metal coordination : bond 0.00211 ( 24) metal coordination : angle 2.14863 ( 36) Misc. bond : bond 0.03162 ( 15) link_NAG-ASN : bond 0.00065 ( 9) link_NAG-ASN : angle 1.77869 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6846 (tt0) cc_final: 0.6503 (tt0) REVERT: A 415 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6748 (mm-40) REVERT: A 592 LYS cc_start: 0.8506 (ttpt) cc_final: 0.7916 (tttm) REVERT: B 160 LYS cc_start: 0.7343 (mtmm) cc_final: 0.7002 (mtmm) REVERT: B 163 GLU cc_start: 0.6834 (tt0) cc_final: 0.6419 (tt0) REVERT: B 592 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7925 (tttm) REVERT: C 163 GLU cc_start: 0.6782 (tt0) cc_final: 0.6237 (tt0) REVERT: C 375 GLU cc_start: 0.7508 (tt0) cc_final: 0.7269 (mt-10) outliers start: 6 outliers final: 6 residues processed: 158 average time/residue: 0.5991 time to fit residues: 104.3282 Evaluate side-chains 135 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 377 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 8 ASN B 236 GLN B 248 GLN C 213 ASN C 248 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100927 restraints weight = 18115.676| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.90 r_work: 0.3072 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14022 Z= 0.184 Angle : 0.587 8.894 18969 Z= 0.283 Chirality : 0.043 0.134 2031 Planarity : 0.005 0.048 2370 Dihedral : 9.222 109.057 2145 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.90 % Allowed : 11.50 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1638 helix: 1.08 (0.25), residues: 438 sheet: 0.24 (0.26), residues: 357 loop : 0.60 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 578 TYR 0.015 0.002 TYR C 40 PHE 0.014 0.002 PHE C 102 TRP 0.017 0.002 TRP C 258 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00450 (13959) covalent geometry : angle 0.54583 (18876) SS BOND : bond 0.00366 ( 15) SS BOND : angle 1.49477 ( 30) hydrogen bonds : bond 0.04216 ( 555) hydrogen bonds : angle 5.23453 ( 1584) metal coordination : bond 0.00577 ( 24) metal coordination : angle 4.47289 ( 36) Misc. bond : bond 0.00076 ( 15) link_NAG-ASN : bond 0.00218 ( 9) link_NAG-ASN : angle 2.09706 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.390 Fit side-chains REVERT: A 140 MET cc_start: 0.6604 (mmt) cc_final: 0.6285 (mmt) REVERT: A 163 GLU cc_start: 0.6859 (tt0) cc_final: 0.6310 (tt0) REVERT: A 592 LYS cc_start: 0.8547 (ttpt) cc_final: 0.7840 (tttm) REVERT: B 12 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7617 (mm-40) REVERT: B 160 LYS cc_start: 0.6929 (mtmm) cc_final: 0.6381 (pttm) REVERT: B 163 GLU cc_start: 0.6754 (tt0) cc_final: 0.6441 (tt0) REVERT: C 12 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7464 (mm-40) REVERT: C 163 GLU cc_start: 0.6630 (tt0) cc_final: 0.6099 (tt0) outliers start: 13 outliers final: 6 residues processed: 142 average time/residue: 0.5418 time to fit residues: 85.2936 Evaluate side-chains 125 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 109 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN C 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101191 restraints weight = 18224.939| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.88 r_work: 0.3077 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14022 Z= 0.159 Angle : 0.548 7.616 18969 Z= 0.267 Chirality : 0.042 0.133 2031 Planarity : 0.004 0.040 2370 Dihedral : 8.654 99.302 2139 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.80 % Allowed : 12.34 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1638 helix: 1.09 (0.25), residues: 438 sheet: 0.18 (0.26), residues: 357 loop : 0.62 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 578 TYR 0.014 0.002 TYR C 40 PHE 0.013 0.002 PHE C 102 TRP 0.015 0.002 TRP C 258 HIS 0.003 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00386 (13959) covalent geometry : angle 0.51828 (18876) SS BOND : bond 0.00286 ( 15) SS BOND : angle 1.37136 ( 30) hydrogen bonds : bond 0.03799 ( 555) hydrogen bonds : angle 5.07931 ( 1584) metal coordination : bond 0.00480 ( 24) metal coordination : angle 3.56455 ( 36) Misc. bond : bond 0.00053 ( 15) link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 2.06333 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.517 Fit side-chains REVERT: A 46 MET cc_start: 0.8952 (mmm) cc_final: 0.8581 (mmt) REVERT: A 140 MET cc_start: 0.6575 (mmt) cc_final: 0.6282 (mmt) REVERT: A 163 GLU cc_start: 0.6831 (tt0) cc_final: 0.6298 (tt0) REVERT: A 544 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6894 (mttp) REVERT: A 592 LYS cc_start: 0.8586 (ttpt) cc_final: 0.7888 (tttm) REVERT: B 12 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7555 (mm-40) REVERT: B 160 LYS cc_start: 0.7056 (mtmm) cc_final: 0.6492 (pttm) REVERT: B 163 GLU cc_start: 0.6719 (tt0) cc_final: 0.6402 (tt0) REVERT: B 544 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6855 (mttp) REVERT: B 578 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6995 (mtt180) REVERT: C 12 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7410 (mm-40) REVERT: C 163 GLU cc_start: 0.6659 (tt0) cc_final: 0.6124 (tt0) REVERT: C 512 LEU cc_start: 0.7429 (mt) cc_final: 0.6832 (tt) REVERT: C 544 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6888 (mtmt) outliers start: 26 outliers final: 9 residues processed: 148 average time/residue: 0.5474 time to fit residues: 90.1770 Evaluate side-chains 139 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 80 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100747 restraints weight = 18126.792| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.89 r_work: 0.3069 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14022 Z= 0.163 Angle : 0.550 7.218 18969 Z= 0.269 Chirality : 0.042 0.134 2031 Planarity : 0.004 0.041 2370 Dihedral : 8.455 92.702 2139 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.36 % Allowed : 12.82 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.21), residues: 1638 helix: 1.08 (0.25), residues: 438 sheet: 0.16 (0.26), residues: 357 loop : 0.63 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 578 TYR 0.014 0.002 TYR C 40 PHE 0.013 0.002 PHE C 102 TRP 0.015 0.002 TRP C 258 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00396 (13959) covalent geometry : angle 0.52353 (18876) SS BOND : bond 0.00271 ( 15) SS BOND : angle 1.36926 ( 30) hydrogen bonds : bond 0.03720 ( 555) hydrogen bonds : angle 5.02400 ( 1584) metal coordination : bond 0.00430 ( 24) metal coordination : angle 3.26358 ( 36) Misc. bond : bond 0.00059 ( 15) link_NAG-ASN : bond 0.00220 ( 9) link_NAG-ASN : angle 2.08277 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6835 (tt0) cc_final: 0.6320 (tt0) REVERT: A 304 MET cc_start: 0.6151 (ttt) cc_final: 0.5758 (tmt) REVERT: A 375 GLU cc_start: 0.7917 (tt0) cc_final: 0.7442 (tt0) REVERT: A 592 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7909 (tttm) REVERT: B 12 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7548 (mm-40) REVERT: B 160 LYS cc_start: 0.7003 (mtmm) cc_final: 0.6439 (pttm) REVERT: B 163 GLU cc_start: 0.6767 (tt0) cc_final: 0.6460 (tt0) REVERT: B 578 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6902 (mtt180) REVERT: C 12 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7436 (mm-40) REVERT: C 140 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.4458 (mmt) REVERT: C 160 LYS cc_start: 0.6702 (mtmm) cc_final: 0.5845 (mttt) REVERT: C 163 GLU cc_start: 0.6682 (tt0) cc_final: 0.6125 (tt0) REVERT: C 544 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6909 (mtmt) outliers start: 34 outliers final: 21 residues processed: 157 average time/residue: 0.5605 time to fit residues: 97.6975 Evaluate side-chains 151 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 126 optimal weight: 0.0570 chunk 127 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100958 restraints weight = 17947.771| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.88 r_work: 0.3084 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14022 Z= 0.128 Angle : 0.515 6.444 18969 Z= 0.252 Chirality : 0.041 0.133 2031 Planarity : 0.005 0.068 2370 Dihedral : 8.141 86.673 2139 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.36 % Allowed : 13.72 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1638 helix: 1.21 (0.25), residues: 438 sheet: 0.16 (0.26), residues: 357 loop : 0.69 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 578 TYR 0.012 0.001 TYR C 40 PHE 0.012 0.001 PHE C 102 TRP 0.013 0.001 TRP C 258 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00305 (13959) covalent geometry : angle 0.49350 (18876) SS BOND : bond 0.00243 ( 15) SS BOND : angle 1.19923 ( 30) hydrogen bonds : bond 0.03409 ( 555) hydrogen bonds : angle 4.88356 ( 1584) metal coordination : bond 0.00376 ( 24) metal coordination : angle 2.86985 ( 36) Misc. bond : bond 0.00035 ( 15) link_NAG-ASN : bond 0.00123 ( 9) link_NAG-ASN : angle 1.85135 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.540 Fit side-chains REVERT: A 160 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6287 (pttm) REVERT: A 163 GLU cc_start: 0.6844 (tt0) cc_final: 0.6369 (tt0) REVERT: A 375 GLU cc_start: 0.7904 (tt0) cc_final: 0.7406 (tt0) REVERT: A 544 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6936 (mtmt) REVERT: A 592 LYS cc_start: 0.8596 (ttpt) cc_final: 0.7868 (tttm) REVERT: B 160 LYS cc_start: 0.7019 (mtmm) cc_final: 0.6492 (pttm) REVERT: B 163 GLU cc_start: 0.6761 (tt0) cc_final: 0.6430 (tt0) REVERT: B 578 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6909 (mtt180) REVERT: C 160 LYS cc_start: 0.6681 (mtmm) cc_final: 0.5876 (mttt) REVERT: C 544 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6864 (mtmt) outliers start: 34 outliers final: 23 residues processed: 152 average time/residue: 0.5658 time to fit residues: 95.2734 Evaluate side-chains 144 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098092 restraints weight = 17669.635| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.92 r_work: 0.3054 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14022 Z= 0.192 Angle : 0.574 7.214 18969 Z= 0.280 Chirality : 0.043 0.137 2031 Planarity : 0.005 0.044 2370 Dihedral : 8.373 86.863 2139 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.29 % Allowed : 13.79 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.21), residues: 1638 helix: 1.02 (0.25), residues: 438 sheet: 0.11 (0.26), residues: 357 loop : 0.61 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 578 TYR 0.016 0.002 TYR C 40 PHE 0.014 0.002 PHE C 102 TRP 0.015 0.002 TRP C 258 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00473 (13959) covalent geometry : angle 0.54727 (18876) SS BOND : bond 0.00296 ( 15) SS BOND : angle 1.60636 ( 30) hydrogen bonds : bond 0.03866 ( 555) hydrogen bonds : angle 5.06415 ( 1584) metal coordination : bond 0.00485 ( 24) metal coordination : angle 3.23472 ( 36) Misc. bond : bond 0.00056 ( 15) link_NAG-ASN : bond 0.00283 ( 9) link_NAG-ASN : angle 2.21967 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6889 (tt0) cc_final: 0.6399 (tt0) REVERT: A 304 MET cc_start: 0.6086 (ttt) cc_final: 0.5704 (tmt) REVERT: A 375 GLU cc_start: 0.7925 (tt0) cc_final: 0.7445 (tt0) REVERT: A 592 LYS cc_start: 0.8630 (ttpt) cc_final: 0.7915 (tttm) REVERT: B 160 LYS cc_start: 0.6996 (mtmm) cc_final: 0.6424 (pttm) REVERT: B 163 GLU cc_start: 0.6798 (tt0) cc_final: 0.6475 (tt0) REVERT: B 544 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6999 (mttp) REVERT: C 160 LYS cc_start: 0.6773 (mtmm) cc_final: 0.5910 (mttt) outliers start: 33 outliers final: 25 residues processed: 148 average time/residue: 0.4989 time to fit residues: 82.9042 Evaluate side-chains 147 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 543 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099607 restraints weight = 17778.709| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.90 r_work: 0.3064 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14022 Z= 0.165 Angle : 0.547 6.583 18969 Z= 0.268 Chirality : 0.042 0.133 2031 Planarity : 0.005 0.041 2370 Dihedral : 8.268 86.054 2139 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.36 % Allowed : 14.00 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1638 helix: 1.10 (0.25), residues: 438 sheet: 0.00 (0.26), residues: 363 loop : 0.64 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 578 TYR 0.014 0.002 TYR B 40 PHE 0.013 0.002 PHE C 102 TRP 0.014 0.002 TRP C 258 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00403 (13959) covalent geometry : angle 0.52428 (18876) SS BOND : bond 0.00285 ( 15) SS BOND : angle 1.46229 ( 30) hydrogen bonds : bond 0.03641 ( 555) hydrogen bonds : angle 4.98393 ( 1584) metal coordination : bond 0.00450 ( 24) metal coordination : angle 2.94625 ( 36) Misc. bond : bond 0.00045 ( 15) link_NAG-ASN : bond 0.00212 ( 9) link_NAG-ASN : angle 2.07349 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6883 (tt0) cc_final: 0.6359 (tt0) REVERT: A 304 MET cc_start: 0.6005 (ttt) cc_final: 0.5658 (tmt) REVERT: A 353 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 375 GLU cc_start: 0.7897 (tt0) cc_final: 0.7408 (tt0) REVERT: A 592 LYS cc_start: 0.8608 (ttpt) cc_final: 0.7886 (tttm) REVERT: B 160 LYS cc_start: 0.6997 (mtmm) cc_final: 0.6458 (pttm) REVERT: B 163 GLU cc_start: 0.6762 (tt0) cc_final: 0.6444 (tt0) REVERT: B 353 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8223 (tt) REVERT: B 578 ARG cc_start: 0.7324 (mtt180) cc_final: 0.6898 (mtt180) REVERT: C 160 LYS cc_start: 0.6704 (mtmm) cc_final: 0.5849 (mttt) outliers start: 34 outliers final: 25 residues processed: 155 average time/residue: 0.5545 time to fit residues: 95.4236 Evaluate side-chains 150 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 543 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.145496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100197 restraints weight = 17720.089| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.90 r_work: 0.3076 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14022 Z= 0.137 Angle : 0.528 7.358 18969 Z= 0.259 Chirality : 0.041 0.133 2031 Planarity : 0.005 0.120 2370 Dihedral : 8.089 83.074 2139 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.73 % Allowed : 14.97 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1638 helix: 1.15 (0.25), residues: 438 sheet: 0.08 (0.27), residues: 357 loop : 0.69 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 578 TYR 0.013 0.001 TYR C 40 PHE 0.012 0.001 PHE C 102 TRP 0.014 0.001 TRP C 258 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00329 (13959) covalent geometry : angle 0.50747 (18876) SS BOND : bond 0.00251 ( 15) SS BOND : angle 1.32222 ( 30) hydrogen bonds : bond 0.03448 ( 555) hydrogen bonds : angle 4.90322 ( 1584) metal coordination : bond 0.00388 ( 24) metal coordination : angle 2.78200 ( 36) Misc. bond : bond 0.00034 ( 15) link_NAG-ASN : bond 0.00149 ( 9) link_NAG-ASN : angle 1.93199 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6889 (tt0) cc_final: 0.6409 (tt0) REVERT: A 304 MET cc_start: 0.6027 (ttt) cc_final: 0.5705 (tmt) REVERT: A 353 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 375 GLU cc_start: 0.7870 (tt0) cc_final: 0.7385 (tt0) REVERT: A 544 LYS cc_start: 0.7395 (tppp) cc_final: 0.6971 (mtmt) REVERT: A 592 LYS cc_start: 0.8595 (ttpt) cc_final: 0.7886 (tttm) REVERT: B 160 LYS cc_start: 0.7006 (mtmm) cc_final: 0.6454 (pttm) REVERT: B 163 GLU cc_start: 0.6726 (tt0) cc_final: 0.6402 (tt0) REVERT: B 353 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 578 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6917 (mtt180) REVERT: C 160 LYS cc_start: 0.6696 (mtmm) cc_final: 0.5884 (mttt) outliers start: 25 outliers final: 22 residues processed: 151 average time/residue: 0.5443 time to fit residues: 91.3994 Evaluate side-chains 149 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098573 restraints weight = 17919.290| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.93 r_work: 0.3057 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14022 Z= 0.184 Angle : 0.570 10.229 18969 Z= 0.279 Chirality : 0.043 0.136 2031 Planarity : 0.005 0.100 2370 Dihedral : 8.300 84.098 2139 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 14.41 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.21), residues: 1638 helix: 0.98 (0.25), residues: 438 sheet: -0.01 (0.26), residues: 363 loop : 0.64 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 578 TYR 0.015 0.002 TYR C 40 PHE 0.013 0.002 PHE C 102 TRP 0.015 0.002 TRP C 258 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00453 (13959) covalent geometry : angle 0.54620 (18876) SS BOND : bond 0.00298 ( 15) SS BOND : angle 1.57534 ( 30) hydrogen bonds : bond 0.03774 ( 555) hydrogen bonds : angle 5.04680 ( 1584) metal coordination : bond 0.00464 ( 24) metal coordination : angle 3.07974 ( 36) Misc. bond : bond 0.00050 ( 15) link_NAG-ASN : bond 0.00262 ( 9) link_NAG-ASN : angle 2.14359 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6903 (tt0) cc_final: 0.6390 (tt0) REVERT: A 353 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 375 GLU cc_start: 0.7881 (tt0) cc_final: 0.7388 (tt0) REVERT: A 592 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7918 (tttm) REVERT: B 160 LYS cc_start: 0.6997 (mtmm) cc_final: 0.6444 (pttm) REVERT: B 163 GLU cc_start: 0.6762 (tt0) cc_final: 0.6430 (tt0) REVERT: B 353 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8234 (tt) REVERT: B 578 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6942 (mtt180) REVERT: C 160 LYS cc_start: 0.6781 (mtmm) cc_final: 0.5932 (mttt) REVERT: C 500 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6060 (ptp-110) outliers start: 31 outliers final: 25 residues processed: 150 average time/residue: 0.5316 time to fit residues: 89.1878 Evaluate side-chains 151 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 500 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 124 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 157 optimal weight: 0.0060 chunk 102 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099389 restraints weight = 17769.537| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.92 r_work: 0.3078 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14022 Z= 0.131 Angle : 0.535 14.732 18969 Z= 0.260 Chirality : 0.041 0.169 2031 Planarity : 0.005 0.092 2370 Dihedral : 8.040 80.864 2139 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.94 % Allowed : 14.76 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.21), residues: 1638 helix: 1.11 (0.25), residues: 438 sheet: 0.09 (0.27), residues: 357 loop : 0.72 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 578 TYR 0.012 0.001 TYR B 40 PHE 0.013 0.001 PHE B 436 TRP 0.013 0.001 TRP C 258 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00314 (13959) covalent geometry : angle 0.51500 (18876) SS BOND : bond 0.00253 ( 15) SS BOND : angle 1.37311 ( 30) hydrogen bonds : bond 0.03389 ( 555) hydrogen bonds : angle 4.89906 ( 1584) metal coordination : bond 0.00384 ( 24) metal coordination : angle 2.68625 ( 36) Misc. bond : bond 0.00030 ( 15) link_NAG-ASN : bond 0.00132 ( 9) link_NAG-ASN : angle 1.90017 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6873 (tt0) cc_final: 0.6375 (tt0) REVERT: A 353 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 375 GLU cc_start: 0.7857 (tt0) cc_final: 0.7365 (tt0) REVERT: A 551 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7378 (ttt180) REVERT: A 592 LYS cc_start: 0.8622 (ttpt) cc_final: 0.7920 (tttm) REVERT: B 160 LYS cc_start: 0.7014 (mtmm) cc_final: 0.6477 (pttm) REVERT: B 163 GLU cc_start: 0.6703 (tt0) cc_final: 0.6367 (tt0) REVERT: B 353 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8247 (tt) REVERT: B 551 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7344 (ttt180) REVERT: B 578 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6984 (mtt180) REVERT: C 160 LYS cc_start: 0.6807 (mtmm) cc_final: 0.5944 (mttt) outliers start: 28 outliers final: 25 residues processed: 147 average time/residue: 0.5377 time to fit residues: 88.3093 Evaluate side-chains 150 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.144209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098611 restraints weight = 17720.289| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.92 r_work: 0.3066 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14022 Z= 0.162 Angle : 0.559 14.215 18969 Z= 0.272 Chirality : 0.042 0.167 2031 Planarity : 0.005 0.087 2370 Dihedral : 8.137 79.809 2139 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 14.62 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1638 helix: 1.00 (0.25), residues: 438 sheet: 0.01 (0.26), residues: 363 loop : 0.69 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 578 TYR 0.015 0.002 TYR B 40 PHE 0.013 0.002 PHE C 102 TRP 0.014 0.001 TRP C 258 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00396 (13959) covalent geometry : angle 0.53691 (18876) SS BOND : bond 0.00277 ( 15) SS BOND : angle 1.45988 ( 30) hydrogen bonds : bond 0.03615 ( 555) hydrogen bonds : angle 4.99040 ( 1584) metal coordination : bond 0.00425 ( 24) metal coordination : angle 2.95299 ( 36) Misc. bond : bond 0.00041 ( 15) link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 2.03638 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6145.26 seconds wall clock time: 105 minutes 26.34 seconds (6326.34 seconds total)