Starting phenix.real_space_refine on Thu Jul 31 22:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4s_42976/07_2025/8v4s_42976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4s_42976/07_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_42976/07_2025/8v4s_42976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4s_42976/07_2025/8v4s_42976.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4s_42976/07_2025/8v4s_42976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4s_42976/07_2025/8v4s_42976.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 4, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: C, B Time building chain proxies: 10.97, per 1000 atoms: 0.79 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 C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 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: 4.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.67 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: 5.59 Time building geometry restraints manager: 4.07 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 148.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.210 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.001 TRP B 575 HIS 0.002 0.001 HIS A 85 PHE 0.011 0.002 PHE C 436 TYR 0.015 0.002 TYR B 550 ARG 0.007 0.001 ARG B 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 9) link_NAG-ASN : angle 1.77869 ( 27) hydrogen bonds : bond 0.15198 ( 555) hydrogen bonds : angle 6.53059 ( 1584) metal coordination : bond 0.00211 ( 24) metal coordination : angle 2.14863 ( 36) SS BOND : bond 0.00246 ( 15) SS BOND : angle 1.07516 ( 30) covalent geometry : bond 0.00461 (13959) covalent geometry : angle 0.66366 (18876) Misc. bond : bond 0.03162 ( 15) *********************** 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 : 1.494 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 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: 1.1461 time to fit residues: 200.7060 Evaluate side-chains 134 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 139 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 380 ASN B 8 ASN 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 = 0.3892 r_free = 0.3892 target = 0.144905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099923 restraints weight = 17893.984| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.89 r_work: 0.3052 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14022 Z= 0.242 Angle : 0.639 9.511 18969 Z= 0.308 Chirality : 0.045 0.134 2031 Planarity : 0.005 0.047 2370 Dihedral : 9.460 111.897 2145 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.25 % Allowed : 11.50 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1638 helix: 0.86 (0.25), residues: 438 sheet: 0.13 (0.26), residues: 363 loop : 0.54 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 258 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.002 PHE C 102 TYR 0.017 0.002 TYR C 40 ARG 0.005 0.001 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 9) link_NAG-ASN : angle 2.42651 ( 27) hydrogen bonds : bond 0.04489 ( 555) hydrogen bonds : angle 5.35052 ( 1584) metal coordination : bond 0.00685 ( 24) metal coordination : angle 4.77541 ( 36) SS BOND : bond 0.00346 ( 15) SS BOND : angle 1.72882 ( 30) covalent geometry : bond 0.00598 (13959) covalent geometry : angle 0.59419 (18876) Misc. bond : bond 0.00100 ( 15) *********************** 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 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 2.003 Fit side-chains REVERT: A 140 MET cc_start: 0.6700 (mmt) cc_final: 0.6410 (mmt) REVERT: A 163 GLU cc_start: 0.6918 (tt0) cc_final: 0.6368 (tt0) REVERT: A 592 LYS cc_start: 0.8581 (ttpt) cc_final: 0.7883 (tttm) REVERT: B 12 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7597 (mm-40) REVERT: B 160 LYS cc_start: 0.6908 (mtmm) cc_final: 0.6353 (pttm) REVERT: B 163 GLU cc_start: 0.6773 (tt0) cc_final: 0.6500 (tt0) REVERT: B 592 LYS cc_start: 0.8529 (ttpt) cc_final: 0.7847 (tttm) REVERT: C 12 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7516 (mm-40) outliers start: 18 outliers final: 7 residues processed: 150 average time/residue: 1.2141 time to fit residues: 204.2751 Evaluate side-chains 130 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN B 236 GLN C 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101825 restraints weight = 18092.837| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.87 r_work: 0.3088 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1389 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= 0.133 Angle : 0.524 7.378 18969 Z= 0.256 Chirality : 0.041 0.132 2031 Planarity : 0.004 0.040 2370 Dihedral : 8.651 99.368 2140 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.66 % Allowed : 12.54 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1638 helix: 1.10 (0.25), residues: 438 sheet: 0.18 (0.26), residues: 357 loop : 0.59 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.002 0.000 HIS B 62 PHE 0.012 0.001 PHE C 102 TYR 0.012 0.001 TYR B 40 ARG 0.004 0.000 ARG C 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 9) link_NAG-ASN : angle 1.90803 ( 27) hydrogen bonds : bond 0.03584 ( 555) hydrogen bonds : angle 5.01363 ( 1584) metal coordination : bond 0.00453 ( 24) metal coordination : angle 3.36999 ( 36) SS BOND : bond 0.00267 ( 15) SS BOND : angle 1.23864 ( 30) covalent geometry : bond 0.00317 (13959) covalent geometry : angle 0.49619 (18876) Misc. bond : bond 0.00041 ( 15) *********************** 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 155 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.415 Fit side-chains REVERT: A 140 MET cc_start: 0.6549 (mmt) cc_final: 0.6295 (mmt) REVERT: A 163 GLU cc_start: 0.6808 (tt0) cc_final: 0.6284 (tt0) REVERT: A 512 LEU cc_start: 0.7192 (tp) cc_final: 0.6713 (tt) REVERT: A 544 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6849 (mttp) REVERT: A 592 LYS cc_start: 0.8586 (ttpt) cc_final: 0.7888 (tttm) REVERT: B 160 LYS cc_start: 0.7011 (mtmm) cc_final: 0.6465 (pttm) REVERT: B 163 GLU cc_start: 0.6705 (tt0) cc_final: 0.6380 (tt0) REVERT: B 544 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6823 (mttp) REVERT: B 578 ARG cc_start: 0.7359 (mtt180) cc_final: 0.6969 (mtt180) REVERT: C 544 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6817 (mtmt) outliers start: 24 outliers final: 7 residues processed: 150 average time/residue: 1.0836 time to fit residues: 181.3617 Evaluate side-chains 133 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 415 GLN 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 544 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 129 CYS 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 104 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.144513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099868 restraints weight = 18001.477| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.88 r_work: 0.3055 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14022 Z= 0.218 Angle : 0.596 7.740 18969 Z= 0.292 Chirality : 0.044 0.136 2031 Planarity : 0.005 0.044 2370 Dihedral : 8.835 98.974 2139 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.43 % Allowed : 12.89 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1638 helix: 0.87 (0.25), residues: 438 sheet: 0.04 (0.26), residues: 363 loop : 0.50 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 258 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.002 PHE C 102 TYR 0.016 0.002 TYR C 40 ARG 0.007 0.000 ARG A 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 9) link_NAG-ASN : angle 2.36093 ( 27) hydrogen bonds : bond 0.04083 ( 555) hydrogen bonds : angle 5.19745 ( 1584) metal coordination : bond 0.00516 ( 24) metal coordination : angle 3.62686 ( 36) SS BOND : bond 0.00308 ( 15) SS BOND : angle 1.57948 ( 30) covalent geometry : bond 0.00540 (13959) covalent geometry : angle 0.56603 (18876) Misc. bond : bond 0.00077 ( 15) *********************** 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 163 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.491 Fit side-chains REVERT: A 163 GLU cc_start: 0.6881 (tt0) cc_final: 0.6364 (tt0) REVERT: A 512 LEU cc_start: 0.7183 (tp) cc_final: 0.6741 (tt) REVERT: A 592 LYS cc_start: 0.8612 (ttpt) cc_final: 0.7866 (tttm) REVERT: B 160 LYS cc_start: 0.7016 (mtmm) cc_final: 0.6496 (pttm) REVERT: B 163 GLU cc_start: 0.6749 (tt0) cc_final: 0.6453 (tt0) REVERT: C 140 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.4504 (mmt) REVERT: C 544 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6881 (mtmt) outliers start: 35 outliers final: 22 residues processed: 151 average time/residue: 1.0396 time to fit residues: 176.5403 Evaluate side-chains 147 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.144973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100456 restraints weight = 18122.996| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.87 r_work: 0.3067 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1629 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= 0.176 Angle : 0.559 6.929 18969 Z= 0.273 Chirality : 0.042 0.135 2031 Planarity : 0.005 0.066 2370 Dihedral : 8.616 95.012 2139 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.43 % Allowed : 13.37 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1638 helix: 0.95 (0.25), residues: 438 sheet: 0.04 (0.26), residues: 363 loop : 0.52 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 258 HIS 0.003 0.001 HIS B 62 PHE 0.013 0.002 PHE C 102 TYR 0.015 0.002 TYR B 40 ARG 0.007 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 9) link_NAG-ASN : angle 2.16705 ( 27) hydrogen bonds : bond 0.03766 ( 555) hydrogen bonds : angle 5.08531 ( 1584) metal coordination : bond 0.00475 ( 24) metal coordination : angle 3.21634 ( 36) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.49054 ( 30) covalent geometry : bond 0.00431 (13959) covalent geometry : angle 0.53254 (18876) Misc. bond : bond 0.00051 ( 15) *********************** 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: 35 poor density : 126 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6883 (tt0) cc_final: 0.6386 (tt0) REVERT: A 375 GLU cc_start: 0.7894 (tt0) cc_final: 0.7408 (tt0) REVERT: A 512 LEU cc_start: 0.7191 (tp) cc_final: 0.6772 (tt) REVERT: A 592 LYS cc_start: 0.8600 (ttpt) cc_final: 0.7889 (tttm) REVERT: B 12 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: B 160 LYS cc_start: 0.7023 (mtmm) cc_final: 0.6414 (pttm) REVERT: B 163 GLU cc_start: 0.6776 (tt0) cc_final: 0.6480 (tt0) REVERT: C 140 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.4435 (mmt) REVERT: C 544 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6911 (mtmt) outliers start: 35 outliers final: 23 residues processed: 156 average time/residue: 1.0147 time to fit residues: 178.5784 Evaluate side-chains 148 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 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 129 CYS 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 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 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 66 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.144061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099101 restraints weight = 17910.167| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.89 r_work: 0.3049 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14022 Z= 0.212 Angle : 0.593 7.455 18969 Z= 0.290 Chirality : 0.044 0.136 2031 Planarity : 0.005 0.048 2370 Dihedral : 8.817 95.818 2139 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.22 % Allowed : 14.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1638 helix: 0.85 (0.25), residues: 438 sheet: -0.03 (0.26), residues: 363 loop : 0.47 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 258 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.002 PHE C 102 TYR 0.016 0.002 TYR C 40 ARG 0.005 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 9) link_NAG-ASN : angle 2.38402 ( 27) hydrogen bonds : bond 0.04021 ( 555) hydrogen bonds : angle 5.19842 ( 1584) metal coordination : bond 0.00537 ( 24) metal coordination : angle 3.40672 ( 36) SS BOND : bond 0.00322 ( 15) SS BOND : angle 1.64803 ( 30) covalent geometry : bond 0.00524 (13959) covalent geometry : angle 0.56462 (18876) Misc. bond : bond 0.00061 ( 15) *********************** 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 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6967 (tt0) cc_final: 0.6472 (tt0) REVERT: A 375 GLU cc_start: 0.7887 (tt0) cc_final: 0.7402 (tt0) REVERT: A 512 LEU cc_start: 0.7228 (tp) cc_final: 0.6821 (tt) REVERT: A 592 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7889 (tttm) REVERT: B 12 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7576 (mm-40) REVERT: B 160 LYS cc_start: 0.6984 (mtmm) cc_final: 0.6466 (pttm) REVERT: B 163 GLU cc_start: 0.6796 (tt0) cc_final: 0.6507 (tt0) REVERT: C 140 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.4487 (mmt) REVERT: C 160 LYS cc_start: 0.6651 (mtmm) cc_final: 0.5874 (mttt) REVERT: C 163 GLU cc_start: 0.6667 (tt0) cc_final: 0.6075 (tt0) outliers start: 32 outliers final: 25 residues processed: 146 average time/residue: 1.5427 time to fit residues: 253.0032 Evaluate side-chains 148 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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 12 GLN 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 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 136 ILE Chi-restraints excluded: chain C residue 140 MET 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 132 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.144621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099183 restraints weight = 17758.383| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.90 r_work: 0.3058 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14022 Z= 0.184 Angle : 0.565 6.786 18969 Z= 0.277 Chirality : 0.042 0.135 2031 Planarity : 0.005 0.050 2370 Dihedral : 8.740 94.445 2139 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.29 % Allowed : 14.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1638 helix: 0.93 (0.25), residues: 438 sheet: -0.03 (0.26), residues: 363 loop : 0.50 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 258 HIS 0.002 0.001 HIS A 62 PHE 0.013 0.002 PHE C 102 TYR 0.015 0.002 TYR B 40 ARG 0.004 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 9) link_NAG-ASN : angle 2.20633 ( 27) hydrogen bonds : bond 0.03782 ( 555) hydrogen bonds : angle 5.09775 ( 1584) metal coordination : bond 0.00491 ( 24) metal coordination : angle 3.09996 ( 36) SS BOND : bond 0.00301 ( 15) SS BOND : angle 1.62419 ( 30) covalent geometry : bond 0.00452 (13959) covalent geometry : angle 0.53962 (18876) Misc. bond : bond 0.00050 ( 15) *********************** 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 157 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6921 (tt0) cc_final: 0.6433 (tt0) REVERT: A 375 GLU cc_start: 0.7863 (tt0) cc_final: 0.7387 (tt0) REVERT: A 512 LEU cc_start: 0.7192 (tp) cc_final: 0.6801 (tt) REVERT: A 592 LYS cc_start: 0.8619 (ttpt) cc_final: 0.7914 (tttm) REVERT: B 160 LYS cc_start: 0.7013 (mtmm) cc_final: 0.6434 (pttm) REVERT: B 163 GLU cc_start: 0.6797 (tt0) cc_final: 0.6500 (tt0) REVERT: C 140 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.4462 (mmt) REVERT: C 160 LYS cc_start: 0.6635 (mtmm) cc_final: 0.5784 (mttt) REVERT: C 544 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7020 (mtmt) outliers start: 33 outliers final: 27 residues processed: 152 average time/residue: 1.5730 time to fit residues: 266.5932 Evaluate side-chains 149 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 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 19 THR 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 274 SER 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 140 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 164 optimal weight: 0.0050 overall best weight: 0.2750 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.145960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100652 restraints weight = 17774.049| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.93 r_work: 0.3099 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14022 Z= 0.100 Angle : 0.488 5.493 18969 Z= 0.240 Chirality : 0.040 0.125 2031 Planarity : 0.004 0.048 2370 Dihedral : 7.975 82.799 2139 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.94 % Allowed : 14.83 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1638 helix: 1.24 (0.25), residues: 438 sheet: 0.07 (0.27), residues: 357 loop : 0.65 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 575 HIS 0.001 0.000 HIS A 62 PHE 0.009 0.001 PHE A 436 TYR 0.010 0.001 TYR C 40 ARG 0.004 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 9) link_NAG-ASN : angle 1.66900 ( 27) hydrogen bonds : bond 0.03100 ( 555) hydrogen bonds : angle 4.76331 ( 1584) metal coordination : bond 0.00333 ( 24) metal coordination : angle 2.42740 ( 36) SS BOND : bond 0.00223 ( 15) SS BOND : angle 1.12996 ( 30) covalent geometry : bond 0.00233 (13959) covalent geometry : angle 0.47115 (18876) Misc. bond : bond 0.00017 ( 15) *********************** 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 158 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6815 (tt0) cc_final: 0.6377 (tt0) REVERT: A 353 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 375 GLU cc_start: 0.7879 (tt0) cc_final: 0.7395 (tt0) REVERT: A 415 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6666 (mm-40) REVERT: A 544 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7059 (mtmt) REVERT: A 592 LYS cc_start: 0.8623 (ttpt) cc_final: 0.7898 (tttm) REVERT: B 160 LYS cc_start: 0.7039 (mtmm) cc_final: 0.6494 (pttm) REVERT: B 163 GLU cc_start: 0.6718 (tt0) cc_final: 0.6396 (tt0) REVERT: B 578 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6963 (mtt180) REVERT: C 160 LYS cc_start: 0.6718 (mtmm) cc_final: 0.5834 (mttt) REVERT: C 544 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7019 (mtmt) outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 1.2105 time to fit residues: 208.5944 Evaluate side-chains 146 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 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 A residue 544 LYS Chi-restraints excluded: chain B residue 19 THR 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 377 CYS 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 377 CYS Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 27 optimal weight: 0.9990 chunk 135 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.144251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098650 restraints weight = 17725.089| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.91 r_work: 0.3063 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14022 Z= 0.172 Angle : 0.553 6.432 18969 Z= 0.272 Chirality : 0.042 0.138 2031 Planarity : 0.006 0.133 2370 Dihedral : 8.227 81.865 2139 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.01 % Allowed : 14.76 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1638 helix: 1.07 (0.25), residues: 438 sheet: 0.00 (0.26), residues: 363 loop : 0.63 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 258 HIS 0.002 0.001 HIS B 62 PHE 0.014 0.002 PHE C 102 TYR 0.015 0.002 TYR C 40 ARG 0.009 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 9) link_NAG-ASN : angle 2.06235 ( 27) hydrogen bonds : bond 0.03677 ( 555) hydrogen bonds : angle 4.99044 ( 1584) metal coordination : bond 0.00428 ( 24) metal coordination : angle 2.94643 ( 36) SS BOND : bond 0.00279 ( 15) SS BOND : angle 1.40547 ( 30) covalent geometry : bond 0.00422 (13959) covalent geometry : angle 0.53069 (18876) Misc. bond : bond 0.00043 ( 15) *********************** 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: 29 poor density : 129 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6894 (tt0) cc_final: 0.6422 (tt0) REVERT: A 375 GLU cc_start: 0.7878 (tt0) cc_final: 0.7403 (tt0) REVERT: A 551 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7563 (mtp180) REVERT: A 592 LYS cc_start: 0.8627 (ttpt) cc_final: 0.7918 (tttm) REVERT: B 160 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6482 (pttm) REVERT: B 163 GLU cc_start: 0.6727 (tt0) cc_final: 0.6389 (tt0) REVERT: B 578 ARG cc_start: 0.7346 (mtt180) cc_final: 0.6918 (mtt180) REVERT: C 160 LYS cc_start: 0.6702 (mtmm) cc_final: 0.5876 (mttt) REVERT: C 544 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7011 (mtmt) REVERT: C 551 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7343 (ttt180) outliers start: 29 outliers final: 24 residues processed: 150 average time/residue: 1.0607 time to fit residues: 177.6491 Evaluate side-chains 153 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 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 19 THR 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 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 377 CYS Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 0.9990 chunk 131 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 127 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 0.0020 overall best weight: 0.2788 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.145991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101044 restraints weight = 17842.783| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.92 r_work: 0.3099 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14022 Z= 0.101 Angle : 0.491 5.550 18969 Z= 0.241 Chirality : 0.040 0.127 2031 Planarity : 0.005 0.112 2370 Dihedral : 7.717 78.984 2139 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.52 % Allowed : 15.32 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1638 helix: 1.27 (0.25), residues: 438 sheet: 0.09 (0.26), residues: 357 loop : 0.74 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 575 HIS 0.001 0.000 HIS A 62 PHE 0.010 0.001 PHE C 102 TYR 0.010 0.001 TYR C 40 ARG 0.006 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 9) link_NAG-ASN : angle 1.66538 ( 27) hydrogen bonds : bond 0.03081 ( 555) hydrogen bonds : angle 4.73340 ( 1584) metal coordination : bond 0.00331 ( 24) metal coordination : angle 2.36834 ( 36) SS BOND : bond 0.00296 ( 15) SS BOND : angle 1.19522 ( 30) covalent geometry : bond 0.00236 (13959) covalent geometry : angle 0.47422 (18876) Misc. bond : bond 0.00018 ( 15) ********************** 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 146 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9015 (mmm) cc_final: 0.8694 (mmt) REVERT: A 163 GLU cc_start: 0.6802 (tt0) cc_final: 0.6363 (tt0) REVERT: A 353 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8314 (tt) REVERT: A 375 GLU cc_start: 0.7872 (tt0) cc_final: 0.7383 (tt0) REVERT: A 415 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6624 (mm-40) REVERT: A 592 LYS cc_start: 0.8635 (ttpt) cc_final: 0.7926 (tttm) REVERT: B 160 LYS cc_start: 0.7054 (mtmm) cc_final: 0.6514 (pttm) REVERT: B 163 GLU cc_start: 0.6706 (tt0) cc_final: 0.6381 (tt0) REVERT: C 160 LYS cc_start: 0.6753 (mtmm) cc_final: 0.5871 (mttt) REVERT: C 544 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7035 (mtmt) REVERT: C 551 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7415 (ttt180) outliers start: 22 outliers final: 19 residues processed: 144 average time/residue: 1.1237 time to fit residues: 180.0603 Evaluate side-chains 143 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 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 377 CYS 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 377 CYS Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.144623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099534 restraints weight = 17946.863| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.90 r_work: 0.3056 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14022 Z= 0.189 Angle : 0.568 6.522 18969 Z= 0.279 Chirality : 0.043 0.139 2031 Planarity : 0.006 0.111 2370 Dihedral : 8.152 80.867 2139 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.08 % Allowed : 14.83 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1638 helix: 1.03 (0.25), residues: 438 sheet: 0.12 (0.26), residues: 357 loop : 0.62 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 258 HIS 0.003 0.001 HIS A 62 PHE 0.015 0.002 PHE C 436 TYR 0.015 0.002 TYR C 40 ARG 0.007 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 9) link_NAG-ASN : angle 2.11749 ( 27) hydrogen bonds : bond 0.03769 ( 555) hydrogen bonds : angle 5.01704 ( 1584) metal coordination : bond 0.00454 ( 24) metal coordination : angle 2.99280 ( 36) SS BOND : bond 0.00296 ( 15) SS BOND : angle 1.53967 ( 30) covalent geometry : bond 0.00466 (13959) covalent geometry : angle 0.54536 (18876) Misc. bond : bond 0.00049 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13342.90 seconds wall clock time: 236 minutes 53.01 seconds (14213.01 seconds total)