Starting phenix.real_space_refine on Fri May 16 02:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4s_42976/05_2025/8v4s_42976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4s_42976/05_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_42976/05_2025/8v4s_42976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4s_42976/05_2025/8v4s_42976.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4s_42976/05_2025/8v4s_42976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4s_42976/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.45, per 1000 atoms: 0.90 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: 3.72 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: 1.74 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: 4.51 Time building geometry restraints manager: 4.48 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: 0.09 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: 35.370 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.350 Process input model: 43.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.640 ------------------------------------------------------------------------------- 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 : 1.505 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: 1.1563 time to fit residues: 202.4097 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 : 1.478 ------------------------------------------------------------------------------- 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 = 0.144897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099920 restraints weight = 17894.775| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.89 r_work: 0.3053 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 1.516 Fit side-chains REVERT: A 140 MET cc_start: 0.6693 (mmt) cc_final: 0.6404 (mmt) REVERT: A 163 GLU cc_start: 0.6913 (tt0) cc_final: 0.6362 (tt0) REVERT: A 592 LYS cc_start: 0.8578 (ttpt) cc_final: 0.7879 (tttm) REVERT: B 12 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7593 (mm-40) REVERT: B 160 LYS cc_start: 0.6903 (mtmm) cc_final: 0.6348 (pttm) REVERT: B 163 GLU cc_start: 0.6771 (tt0) cc_final: 0.6497 (tt0) REVERT: B 592 LYS cc_start: 0.8526 (ttpt) cc_final: 0.7842 (tttm) REVERT: C 12 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7512 (mm-40) outliers start: 18 outliers final: 7 residues processed: 150 average time/residue: 1.0093 time to fit residues: 169.6655 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 : 1.452 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 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: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.145658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101001 restraints weight = 18075.065| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.89 r_work: 0.3073 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14022 Z= 0.155 Angle : 0.545 7.624 18969 Z= 0.266 Chirality : 0.042 0.132 2031 Planarity : 0.004 0.041 2370 Dihedral : 8.789 101.492 2140 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.01 % Allowed : 12.20 % 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: 0.73 (0.21), residues: 1638 helix: 1.01 (0.25), residues: 438 sheet: 0.09 (0.26), residues: 363 loop : 0.56 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.003 0.001 HIS B 62 PHE 0.013 0.002 PHE C 102 TYR 0.013 0.001 TYR C 40 ARG 0.004 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 9) link_NAG-ASN : angle 2.06794 ( 27) hydrogen bonds : bond 0.03772 ( 555) hydrogen bonds : angle 5.09892 ( 1584) metal coordination : bond 0.00482 ( 24) metal coordination : angle 3.54583 ( 36) SS BOND : bond 0.00281 ( 15) SS BOND : angle 1.35147 ( 30) covalent geometry : bond 0.00375 (13959) covalent geometry : angle 0.51503 (18876) Misc. bond : bond 0.00052 ( 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 156 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.513 Fit side-chains REVERT: A 140 MET cc_start: 0.6618 (mmt) cc_final: 0.6340 (mmt) REVERT: A 163 GLU cc_start: 0.6865 (tt0) cc_final: 0.6337 (tt0) REVERT: A 512 LEU cc_start: 0.7225 (tp) cc_final: 0.6750 (tt) REVERT: A 592 LYS cc_start: 0.8601 (ttpt) cc_final: 0.7904 (tttm) REVERT: B 160 LYS cc_start: 0.7002 (mtmm) cc_final: 0.6444 (pttm) REVERT: B 163 GLU cc_start: 0.6733 (tt0) cc_final: 0.6414 (tt0) REVERT: B 544 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6864 (mttp) REVERT: C 140 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.4555 (mmt) REVERT: C 544 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6893 (mtmt) outliers start: 29 outliers final: 14 residues processed: 150 average time/residue: 0.9836 time to fit residues: 166.0606 Evaluate side-chains 140 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 543 SER 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: 0.0270 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 118 optimal weight: 0.0040 overall best weight: 0.4850 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.145633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100746 restraints weight = 17689.075| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.89 r_work: 0.3079 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14022 Z= 0.135 Angle : 0.524 6.906 18969 Z= 0.256 Chirality : 0.041 0.134 2031 Planarity : 0.004 0.041 2370 Dihedral : 8.414 93.439 2140 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 13.17 % Favored : 84.75 % 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: 0.84 (0.21), residues: 1638 helix: 1.13 (0.25), residues: 438 sheet: 0.14 (0.26), residues: 357 loop : 0.62 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 258 HIS 0.002 0.000 HIS B 62 PHE 0.012 0.001 PHE C 102 TYR 0.013 0.001 TYR C 40 ARG 0.006 0.000 ARG A 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 9) link_NAG-ASN : angle 1.90897 ( 27) hydrogen bonds : bond 0.03497 ( 555) hydrogen bonds : angle 4.95512 ( 1584) metal coordination : bond 0.00380 ( 24) metal coordination : angle 3.09301 ( 36) SS BOND : bond 0.00299 ( 15) SS BOND : angle 1.25112 ( 30) covalent geometry : bond 0.00323 (13959) covalent geometry : angle 0.49951 (18876) Misc. bond : bond 0.00043 ( 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 164 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.639 Fit side-chains REVERT: A 163 GLU cc_start: 0.6838 (tt0) cc_final: 0.6352 (tt0) REVERT: A 304 MET cc_start: 0.6024 (ttt) cc_final: 0.5556 (ttp) REVERT: A 375 GLU cc_start: 0.7905 (tt0) cc_final: 0.7428 (tt0) REVERT: A 512 LEU cc_start: 0.7199 (tp) cc_final: 0.6759 (tt) REVERT: A 592 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7909 (tttm) REVERT: B 160 LYS cc_start: 0.7017 (mtmm) cc_final: 0.6443 (pttm) REVERT: B 163 GLU cc_start: 0.6734 (tt0) cc_final: 0.6429 (tt0) REVERT: B 544 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6832 (mttp) REVERT: B 578 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6927 (mtt180) REVERT: C 140 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.4472 (mmt) REVERT: C 544 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6904 (mtmt) outliers start: 30 outliers final: 19 residues processed: 155 average time/residue: 1.0339 time to fit residues: 180.0899 Evaluate side-chains 149 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 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: 2.9990 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 146 optimal weight: 0.0070 chunk 23 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 72 optimal weight: 0.1980 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.145385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100443 restraints weight = 17892.700| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.90 r_work: 0.3071 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14022 Z= 0.147 Angle : 0.532 6.597 18969 Z= 0.260 Chirality : 0.041 0.135 2031 Planarity : 0.005 0.066 2370 Dihedral : 8.276 88.043 2140 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.29 % Allowed : 13.86 % Favored : 83.85 % 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: 0.85 (0.21), residues: 1638 helix: 1.13 (0.25), residues: 438 sheet: 0.13 (0.26), residues: 357 loop : 0.64 (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 0.013 0.002 PHE C 102 TYR 0.014 0.001 TYR C 40 ARG 0.006 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 9) link_NAG-ASN : angle 1.97388 ( 27) hydrogen bonds : bond 0.03562 ( 555) hydrogen bonds : angle 4.95261 ( 1584) metal coordination : bond 0.00412 ( 24) metal coordination : angle 3.00394 ( 36) SS BOND : bond 0.00286 ( 15) SS BOND : angle 1.37698 ( 30) covalent geometry : bond 0.00356 (13959) covalent geometry : angle 0.50847 (18876) Misc. bond : bond 0.00043 ( 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 163 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6976 (mtmm) cc_final: 0.6399 (pttm) REVERT: A 163 GLU cc_start: 0.6872 (tt0) cc_final: 0.6389 (tt0) REVERT: A 375 GLU cc_start: 0.7884 (tt0) cc_final: 0.7394 (tt0) REVERT: A 512 LEU cc_start: 0.7161 (tp) cc_final: 0.6766 (tt) REVERT: A 544 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6897 (mttp) REVERT: A 592 LYS cc_start: 0.8593 (ttpt) cc_final: 0.7868 (tttm) REVERT: B 160 LYS cc_start: 0.6988 (mtmm) cc_final: 0.6398 (pttm) REVERT: B 163 GLU cc_start: 0.6750 (tt0) cc_final: 0.6420 (tt0) REVERT: B 578 ARG cc_start: 0.7425 (mtt180) cc_final: 0.7007 (mtt180) REVERT: C 544 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6950 (mtmt) outliers start: 33 outliers final: 26 residues processed: 155 average time/residue: 1.0797 time to fit residues: 187.2360 Evaluate side-chains 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 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 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: 10.0000 chunk 18 optimal weight: 0.9990 chunk 150 optimal weight: 0.0670 chunk 140 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099974 restraints weight = 17891.481| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.91 r_work: 0.3065 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14022 Z= 0.164 Angle : 0.547 6.721 18969 Z= 0.268 Chirality : 0.042 0.136 2031 Planarity : 0.005 0.041 2370 Dihedral : 8.271 85.802 2140 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.22 % Allowed : 14.21 % Favored : 83.58 % 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: 0.81 (0.21), residues: 1638 helix: 1.09 (0.25), residues: 438 sheet: 0.10 (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 B 62 PHE 0.013 0.002 PHE C 102 TYR 0.015 0.002 TYR C 40 ARG 0.005 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 9) link_NAG-ASN : angle 2.06663 ( 27) hydrogen bonds : bond 0.03670 ( 555) hydrogen bonds : angle 4.99840 ( 1584) metal coordination : bond 0.00433 ( 24) metal coordination : angle 2.99215 ( 36) SS BOND : bond 0.00277 ( 15) SS BOND : angle 1.42633 ( 30) covalent geometry : bond 0.00400 (13959) covalent geometry : angle 0.52391 (18876) Misc. bond : bond 0.00047 ( 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 158 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6912 (tt0) cc_final: 0.6441 (tt0) REVERT: A 304 MET cc_start: 0.5885 (ttt) cc_final: 0.5674 (tmt) REVERT: A 375 GLU cc_start: 0.7898 (tt0) cc_final: 0.7411 (tt0) REVERT: A 512 LEU cc_start: 0.7169 (tp) cc_final: 0.6784 (tt) REVERT: A 592 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7886 (tttm) REVERT: B 12 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7580 (mm-40) REVERT: B 160 LYS cc_start: 0.7013 (mtmm) cc_final: 0.6436 (pttm) REVERT: B 163 GLU cc_start: 0.6777 (tt0) cc_final: 0.6441 (tt0) REVERT: B 578 ARG cc_start: 0.7467 (mtt180) cc_final: 0.7028 (mtt180) REVERT: C 12 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: C 160 LYS cc_start: 0.6622 (mtmm) cc_final: 0.5826 (mttt) REVERT: C 163 GLU cc_start: 0.6688 (tt0) cc_final: 0.6470 (tt0) REVERT: C 544 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6957 (mtmt) outliers start: 32 outliers final: 25 residues processed: 152 average time/residue: 0.9775 time to fit residues: 167.8907 Evaluate side-chains 152 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 236 GLN 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 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 12 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.143979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098448 restraints weight = 17795.135| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.92 r_work: 0.3053 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1740 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= 0.200 Angle : 0.580 7.227 18969 Z= 0.284 Chirality : 0.043 0.136 2031 Planarity : 0.005 0.042 2370 Dihedral : 8.585 89.049 2140 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.49 % Allowed : 13.86 % 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: 0.66 (0.21), residues: 1638 helix: 0.97 (0.25), residues: 438 sheet: -0.02 (0.26), residues: 363 loop : 0.55 (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 0.004 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 9) link_NAG-ASN : angle 2.29148 ( 27) hydrogen bonds : bond 0.03912 ( 555) hydrogen bonds : angle 5.10257 ( 1584) metal coordination : bond 0.00506 ( 24) metal coordination : angle 3.23722 ( 36) SS BOND : bond 0.00308 ( 15) SS BOND : angle 1.63889 ( 30) covalent geometry : bond 0.00494 (13959) covalent geometry : angle 0.55382 (18876) Misc. bond : bond 0.00061 ( 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 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6910 (tt0) cc_final: 0.6419 (tt0) REVERT: A 304 MET cc_start: 0.6033 (ttt) cc_final: 0.5610 (tmt) REVERT: A 512 LEU cc_start: 0.7161 (tp) cc_final: 0.6777 (tt) REVERT: A 592 LYS cc_start: 0.8613 (ttpt) cc_final: 0.7922 (tttm) REVERT: B 12 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7594 (mm-40) REVERT: B 160 LYS cc_start: 0.7005 (mtmm) cc_final: 0.6427 (pttm) REVERT: B 163 GLU cc_start: 0.6797 (tt0) cc_final: 0.6489 (tt0) REVERT: C 140 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.4607 (mmt) REVERT: C 160 LYS cc_start: 0.6680 (mtmm) cc_final: 0.5829 (mttt) outliers start: 36 outliers final: 27 residues processed: 147 average time/residue: 0.9678 time to fit residues: 160.8853 Evaluate side-chains 146 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 128 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 164 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.145296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099852 restraints weight = 17760.602| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.92 r_work: 0.3083 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14022 Z= 0.121 Angle : 0.510 5.833 18969 Z= 0.250 Chirality : 0.040 0.130 2031 Planarity : 0.004 0.041 2370 Dihedral : 8.117 82.779 2140 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.08 % Allowed : 14.48 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.21), residues: 1638 helix: 1.21 (0.25), residues: 438 sheet: 0.09 (0.27), residues: 357 loop : 0.65 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 258 HIS 0.002 0.000 HIS B 62 PHE 0.011 0.001 PHE C 102 TYR 0.012 0.001 TYR C 40 ARG 0.004 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 9) link_NAG-ASN : angle 1.84092 ( 27) hydrogen bonds : bond 0.03315 ( 555) hydrogen bonds : angle 4.84709 ( 1584) metal coordination : bond 0.00371 ( 24) metal coordination : angle 2.58253 ( 36) SS BOND : bond 0.00248 ( 15) SS BOND : angle 1.30014 ( 30) covalent geometry : bond 0.00288 (13959) covalent geometry : angle 0.49110 (18876) Misc. bond : bond 0.00030 ( 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 160 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6863 (tt0) cc_final: 0.6395 (tt0) REVERT: A 304 MET cc_start: 0.5963 (ttt) cc_final: 0.5708 (tmt) REVERT: A 375 GLU cc_start: 0.7883 (tt0) cc_final: 0.7389 (tt0) REVERT: A 512 LEU cc_start: 0.7168 (tp) cc_final: 0.6804 (tt) REVERT: A 544 LYS cc_start: 0.7385 (tppp) cc_final: 0.6967 (mtmt) REVERT: A 592 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7890 (tttm) REVERT: B 160 LYS cc_start: 0.7008 (mtmm) cc_final: 0.6468 (pttm) REVERT: B 163 GLU cc_start: 0.6698 (tt0) cc_final: 0.6362 (tt0) REVERT: B 578 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6944 (mtt180) REVERT: C 160 LYS cc_start: 0.6687 (mtmm) cc_final: 0.5814 (mttt) REVERT: C 163 GLU cc_start: 0.6693 (tt0) cc_final: 0.6267 (tt0) REVERT: C 544 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7020 (mtmt) outliers start: 30 outliers final: 22 residues processed: 155 average time/residue: 1.1007 time to fit residues: 190.2652 Evaluate side-chains 149 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 377 CYS 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: 0.4980 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 108 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.144443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098841 restraints weight = 17634.342| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.91 r_work: 0.3065 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14022 Z= 0.164 Angle : 0.546 6.480 18969 Z= 0.268 Chirality : 0.042 0.138 2031 Planarity : 0.005 0.042 2370 Dihedral : 8.187 81.736 2140 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.80 % Allowed : 14.83 % 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: 0.80 (0.21), residues: 1638 helix: 1.11 (0.25), residues: 438 sheet: 0.00 (0.26), residues: 363 loop : 0.65 (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 B 40 ARG 0.003 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 9) link_NAG-ASN : angle 2.05574 ( 27) hydrogen bonds : bond 0.03627 ( 555) hydrogen bonds : angle 4.97090 ( 1584) metal coordination : bond 0.00416 ( 24) metal coordination : angle 2.92575 ( 36) SS BOND : bond 0.00276 ( 15) SS BOND : angle 1.41225 ( 30) covalent geometry : bond 0.00400 (13959) covalent geometry : angle 0.52401 (18876) Misc. bond : bond 0.00042 ( 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 156 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6905 (tt0) cc_final: 0.6431 (tt0) REVERT: A 304 MET cc_start: 0.5962 (ttt) cc_final: 0.5705 (tmt) REVERT: A 512 LEU cc_start: 0.7158 (tp) cc_final: 0.6797 (tt) REVERT: A 592 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7902 (tttm) REVERT: B 160 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6468 (pttm) REVERT: B 163 GLU cc_start: 0.6746 (tt0) cc_final: 0.6409 (tt0) REVERT: B 578 ARG cc_start: 0.7361 (mtt180) cc_final: 0.6945 (mtt180) REVERT: C 160 LYS cc_start: 0.6655 (mtmm) cc_final: 0.5833 (mttt) REVERT: C 163 GLU cc_start: 0.6703 (tt0) cc_final: 0.6241 (tt0) REVERT: C 544 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6976 (mtmt) REVERT: C 551 ARG cc_start: 0.7646 (mtp180) cc_final: 0.7331 (ttt180) outliers start: 26 outliers final: 23 residues processed: 151 average time/residue: 1.0971 time to fit residues: 184.7718 Evaluate side-chains 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 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 377 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 544 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 127 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.144528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098943 restraints weight = 17674.160| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.92 r_work: 0.3069 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14022 Z= 0.150 Angle : 0.535 6.119 18969 Z= 0.262 Chirality : 0.041 0.134 2031 Planarity : 0.004 0.041 2370 Dihedral : 8.111 80.076 2139 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.94 % Allowed : 14.69 % 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: 0.83 (0.21), residues: 1638 helix: 1.15 (0.25), residues: 438 sheet: 0.01 (0.26), residues: 363 loop : 0.67 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.002 0.000 HIS A 62 PHE 0.013 0.002 PHE C 102 TYR 0.014 0.001 TYR B 40 ARG 0.003 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 9) link_NAG-ASN : angle 1.97493 ( 27) hydrogen bonds : bond 0.03505 ( 555) hydrogen bonds : angle 4.92603 ( 1584) metal coordination : bond 0.00404 ( 24) metal coordination : angle 2.75806 ( 36) SS BOND : bond 0.00263 ( 15) SS BOND : angle 1.39559 ( 30) covalent geometry : bond 0.00365 (13959) covalent geometry : angle 0.51430 (18876) Misc. bond : bond 0.00036 ( 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 159 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.6890 (tt0) cc_final: 0.6425 (tt0) REVERT: A 415 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6666 (mm110) REVERT: A 512 LEU cc_start: 0.7197 (tp) cc_final: 0.6842 (tt) REVERT: A 551 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7590 (mtp180) REVERT: A 592 LYS cc_start: 0.8611 (ttpt) cc_final: 0.7915 (tttm) REVERT: B 160 LYS cc_start: 0.7029 (mtmm) cc_final: 0.6487 (pttm) REVERT: B 163 GLU cc_start: 0.6748 (tt0) cc_final: 0.6422 (tt0) REVERT: B 578 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6974 (mtt180) REVERT: C 160 LYS cc_start: 0.6695 (mtmm) cc_final: 0.5823 (mttt) REVERT: C 163 GLU cc_start: 0.6676 (tt0) cc_final: 0.6233 (tt0) REVERT: C 551 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7339 (ttt180) outliers start: 28 outliers final: 24 residues processed: 154 average time/residue: 1.0412 time to fit residues: 178.9501 Evaluate side-chains 154 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 159 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.144631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098977 restraints weight = 17798.267| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.93 r_work: 0.3068 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14022 Z= 0.151 Angle : 0.537 6.181 18969 Z= 0.263 Chirality : 0.041 0.135 2031 Planarity : 0.005 0.090 2370 Dihedral : 8.090 80.033 2139 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.73 % Allowed : 14.90 % 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: 0.83 (0.21), residues: 1638 helix: 1.12 (0.25), residues: 438 sheet: 0.01 (0.26), residues: 363 loop : 0.68 (0.23), residues: 837 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 0.013 0.002 PHE C 102 TYR 0.014 0.001 TYR B 40 ARG 0.009 0.000 ARG C 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 9) link_NAG-ASN : angle 1.99036 ( 27) hydrogen bonds : bond 0.03524 ( 555) hydrogen bonds : angle 4.93201 ( 1584) metal coordination : bond 0.00404 ( 24) metal coordination : angle 2.80326 ( 36) SS BOND : bond 0.00266 ( 15) SS BOND : angle 1.38011 ( 30) covalent geometry : bond 0.00366 (13959) covalent geometry : angle 0.51534 (18876) Misc. bond : bond 0.00035 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11789.19 seconds wall clock time: 205 minutes 18.34 seconds (12318.34 seconds total)