Starting phenix.real_space_refine on Thu Feb 13 04:56:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxb_24727/02_2025/7rxb_24727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxb_24727/02_2025/7rxb_24727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxb_24727/02_2025/7rxb_24727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxb_24727/02_2025/7rxb_24727.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxb_24727/02_2025/7rxb_24727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxb_24727/02_2025/7rxb_24727.cif" } resolution = 3.07 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 32 5.16 5 C 5660 2.51 5 N 1382 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4153 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 8 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 292 Chain: "B" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4153 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 8 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 292 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.15, per 1000 atoms: 0.61 Number of scatterers: 8506 At special positions: 0 Unit cell: (115.02, 74.124, 100.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 6 15.00 O 1426 8.00 N 1382 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 63.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 removed outlier: 4.045A pdb=" N VAL A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 85 removed outlier: 3.843A pdb=" N LYS A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.777A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 174 through 191 removed outlier: 3.629A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.599A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.621A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 311 removed outlier: 3.820A pdb=" N PHE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.627A pdb=" N ILE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.596A pdb=" N VAL A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 380 removed outlier: 3.599A pdb=" N TYR A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.901A pdb=" N ARG A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.710A pdb=" N ARG A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.810A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.589A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.585A pdb=" N SER A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 573 " --> pdb=" O TRP A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 573' Processing helix chain 'A' and resid 574 through 592 removed outlier: 3.619A pdb=" N TRP A 578 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 592 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 630 removed outlier: 3.570A pdb=" N LEU A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.797A pdb=" N ARG A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 717 removed outlier: 4.170A pdb=" N SER A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 716 " --> pdb=" O TRP A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.044A pdb=" N VAL B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 85 removed outlier: 3.843A pdb=" N LYS B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.779A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.630A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.599A pdb=" N THR B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 221 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 removed outlier: 3.620A pdb=" N ARG B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.820A pdb=" N PHE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 removed outlier: 3.627A pdb=" N ILE B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.596A pdb=" N VAL B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 380 removed outlier: 3.598A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.901A pdb=" N ARG B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 441 Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.709A pdb=" N ARG B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 525 removed outlier: 3.810A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.590A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 543 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 568 through 573 removed outlier: 3.586A pdb=" N SER B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 573 " --> pdb=" O TRP B 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 568 through 573' Processing helix chain 'B' and resid 574 through 592 removed outlier: 3.618A pdb=" N TRP B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 630 removed outlier: 3.571A pdb=" N LEU B 610 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.798A pdb=" N ARG B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 717 removed outlier: 4.170A pdb=" N SER B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 716 " --> pdb=" O TRP B 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54 removed outlier: 6.807A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 54 removed outlier: 6.807A pdb=" N VAL B 19 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 139 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG B 21 " --> pdb=" O ASP B 137 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1230 1.30 - 1.43: 2566 1.43 - 1.56: 4866 1.56 - 1.68: 12 1.68 - 1.81: 44 Bond restraints: 8718 Sorted by residual: bond pdb=" C1 PGW B1003 " pdb=" O01 PGW B1003 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 PGW A 802 " pdb=" O01 PGW A 802 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 PGW A 803 " pdb=" O01 PGW A 803 " ideal model delta sigma weight residual 1.332 1.417 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C1 PGW B1004 " pdb=" O01 PGW B1004 " ideal model delta sigma weight residual 1.332 1.417 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 PGW B1001 " pdb=" O01 PGW B1001 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.74e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 11368 2.34 - 4.69: 395 4.69 - 7.03: 83 7.03 - 9.38: 26 9.38 - 11.72: 18 Bond angle restraints: 11890 Sorted by residual: angle pdb=" N ILE A 169 " pdb=" CA ILE A 169 " pdb=" C ILE A 169 " ideal model delta sigma weight residual 111.91 105.97 5.94 8.90e-01 1.26e+00 4.46e+01 angle pdb=" N ILE B 169 " pdb=" CA ILE B 169 " pdb=" C ILE B 169 " ideal model delta sigma weight residual 111.91 106.00 5.91 8.90e-01 1.26e+00 4.40e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" O11 PGW B1001 " pdb=" P PGW B1001 " pdb=" O12 PGW B1001 " ideal model delta sigma weight residual 98.90 110.62 -11.72 3.00e+00 1.11e-01 1.53e+01 ... (remaining 11885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 4856 30.26 - 60.53: 160 60.53 - 90.79: 10 90.79 - 121.05: 4 121.05 - 151.32: 4 Dihedral angle restraints: 5034 sinusoidal: 1804 harmonic: 3230 Sorted by residual: dihedral pdb=" CA PHE B 399 " pdb=" C PHE B 399 " pdb=" N HIS B 400 " pdb=" CA HIS B 400 " ideal model delta harmonic sigma weight residual 180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 399 " pdb=" C PHE A 399 " pdb=" N HIS A 400 " pdb=" CA HIS A 400 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASN A 171 " pdb=" C ASN A 171 " pdb=" N THR A 172 " pdb=" CA THR A 172 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 663 0.037 - 0.073: 527 0.073 - 0.110: 130 0.110 - 0.146: 68 0.146 - 0.183: 12 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR B 159 " pdb=" N THR B 159 " pdb=" C THR B 159 " pdb=" CB THR B 159 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA THR A 159 " pdb=" N THR A 159 " pdb=" C THR A 159 " pdb=" CB THR A 159 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA SER A 526 " pdb=" N SER A 526 " pdb=" C SER A 526 " pdb=" CB SER A 526 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 1397 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 422 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 423 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 422 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO A 423 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 377 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.040 5.00e-02 4.00e+02 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3351 2.93 - 3.42: 7552 3.42 - 3.91: 12800 3.91 - 4.41: 14692 4.41 - 4.90: 25955 Nonbonded interactions: 64350 Sorted by model distance: nonbonded pdb=" O SER A 209 " pdb=" OG1 THR A 213 " model vdw 2.437 3.040 nonbonded pdb=" O SER B 209 " pdb=" OG1 THR B 213 " model vdw 2.437 3.040 nonbonded pdb=" O THR B 613 " pdb=" OG SER B 617 " model vdw 2.448 3.040 nonbonded pdb=" O THR A 613 " pdb=" OG SER A 617 " model vdw 2.448 3.040 nonbonded pdb=" O01 PGW B1002 " pdb=" O11 PGW B1002 " model vdw 2.452 2.432 ... (remaining 64345 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 717 or (resid 801 and (name C01 or name C02 or \ name C03 or name C19 or name O03 or name O04 or name O11 or name O12 or name O13 \ or name O14 or name P )) or (resid 802 and (name C01 or name C02 or name C03 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name O0 \ 3 or name O04)) or (resid 803 and (name C01 or name C02 or name C03 or name C1 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C3 or name C4 or name C5 or name C6 or name O01 or name O0 \ 2 or name O03 or name O04)) or resid 804)) selection = (chain 'B' and (resid 11 through 717 or (resid 1001 and (name C01 or name C02 or \ name C03 or name C19 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )) or (resid 1002 and (name C01 or name C02 or name C03 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ O03 or name O04)) or resid 1003 or (resid 1004 and (name C01 or name C02 or name \ C03 or name C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name O01 or name O02 or name O03 or name O04 or nam \ e O11 or name O12 or name O13 or name O14 or name P )))) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.400 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.009 0.087 8718 Z= 0.611 Angle : 1.151 11.724 11890 Z= 0.569 Chirality : 0.055 0.183 1400 Planarity : 0.008 0.079 1438 Dihedral : 16.228 151.317 2926 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.88 (0.18), residues: 1060 helix: -3.22 (0.13), residues: 710 sheet: -0.67 (0.61), residues: 44 loop : -3.09 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 227 HIS 0.008 0.002 HIS A 130 PHE 0.016 0.002 PHE A 140 TYR 0.014 0.002 TYR A 589 ARG 0.006 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.899 Fit side-chains REVERT: A 551 ILE cc_start: 0.8368 (tt) cc_final: 0.7892 (tp) REVERT: B 21 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8075 (ttp-170) REVERT: B 551 ILE cc_start: 0.8344 (tt) cc_final: 0.7954 (tt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1746 time to fit residues: 20.7153 Evaluate side-chains 64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 370 ASN A 518 GLN B 280 GLN B 370 ASN B 518 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.084072 restraints weight = 10476.921| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.57 r_work: 0.2673 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8718 Z= 0.242 Angle : 0.563 8.006 11890 Z= 0.300 Chirality : 0.040 0.121 1400 Planarity : 0.006 0.059 1438 Dihedral : 15.265 124.899 1326 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.50 % Allowed : 7.05 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.24), residues: 1060 helix: -1.45 (0.18), residues: 714 sheet: -0.52 (0.58), residues: 44 loop : -2.52 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 227 HIS 0.004 0.001 HIS B 619 PHE 0.008 0.001 PHE A 286 TYR 0.014 0.001 TYR B 589 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.910 Fit side-chains REVERT: B 21 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8130 (ttp-170) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.1560 time to fit residues: 18.8932 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.113732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.083910 restraints weight = 10566.046| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.59 r_work: 0.2666 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8718 Z= 0.249 Angle : 0.548 7.632 11890 Z= 0.291 Chirality : 0.041 0.129 1400 Planarity : 0.005 0.052 1438 Dihedral : 14.160 118.507 1326 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.88 % Allowed : 10.58 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.26), residues: 1060 helix: -0.77 (0.20), residues: 718 sheet: -0.20 (0.59), residues: 44 loop : -2.38 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 227 HIS 0.004 0.001 HIS B 130 PHE 0.008 0.001 PHE A 286 TYR 0.013 0.001 TYR B 589 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.903 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.1492 time to fit residues: 17.0277 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 509 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.118157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.088379 restraints weight = 10409.053| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.60 r_work: 0.2735 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8718 Z= 0.128 Angle : 0.474 7.427 11890 Z= 0.251 Chirality : 0.038 0.139 1400 Planarity : 0.004 0.043 1438 Dihedral : 12.933 108.657 1326 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.76 % Allowed : 11.08 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.27), residues: 1060 helix: -0.18 (0.21), residues: 706 sheet: 0.12 (0.63), residues: 44 loop : -1.93 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.002 0.001 HIS B 619 PHE 0.007 0.001 PHE A 615 TYR 0.008 0.001 TYR A 180 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.997 Fit side-chains REVERT: B 241 LYS cc_start: 0.8663 (tptp) cc_final: 0.8462 (tttm) outliers start: 6 outliers final: 1 residues processed: 76 average time/residue: 0.1782 time to fit residues: 20.1966 Evaluate side-chains 62 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.114843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.084985 restraints weight = 10408.337| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.57 r_work: 0.2671 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8718 Z= 0.240 Angle : 0.526 7.492 11890 Z= 0.278 Chirality : 0.041 0.127 1400 Planarity : 0.004 0.040 1438 Dihedral : 12.886 108.014 1326 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.13 % Allowed : 10.83 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.27), residues: 1060 helix: -0.12 (0.21), residues: 718 sheet: 0.57 (0.67), residues: 44 loop : -2.09 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.005 0.001 HIS A 619 PHE 0.008 0.001 PHE A 286 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.878 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.1387 time to fit residues: 16.4792 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.113670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.083831 restraints weight = 10378.380| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.57 r_work: 0.2659 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8718 Z= 0.268 Angle : 0.541 7.408 11890 Z= 0.287 Chirality : 0.041 0.145 1400 Planarity : 0.005 0.041 1438 Dihedral : 12.754 108.327 1326 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.39 % Allowed : 10.71 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.27), residues: 1060 helix: -0.06 (0.21), residues: 718 sheet: 0.95 (0.75), residues: 44 loop : -2.09 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.005 0.001 HIS A 619 PHE 0.008 0.001 PHE B 616 TYR 0.011 0.001 TYR B 589 ARG 0.001 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.966 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 0.1523 time to fit residues: 17.9939 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 106 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.117931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.088224 restraints weight = 10317.681| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.59 r_work: 0.2724 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8718 Z= 0.136 Angle : 0.470 7.420 11890 Z= 0.249 Chirality : 0.038 0.129 1400 Planarity : 0.004 0.040 1438 Dihedral : 11.832 102.880 1326 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.76 % Allowed : 11.71 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.27), residues: 1060 helix: 0.38 (0.21), residues: 708 sheet: 0.98 (0.73), residues: 44 loop : -1.90 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.002 0.001 HIS B 619 PHE 0.008 0.001 PHE A 615 TYR 0.009 0.001 TYR B 180 ARG 0.001 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 1.011 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.1372 time to fit residues: 16.4368 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 565 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.115233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.085284 restraints weight = 10527.774| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.59 r_work: 0.2679 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8718 Z= 0.231 Angle : 0.512 7.447 11890 Z= 0.270 Chirality : 0.040 0.129 1400 Planarity : 0.004 0.039 1438 Dihedral : 11.925 104.688 1326 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.26 % Allowed : 11.34 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.27), residues: 1060 helix: 0.30 (0.21), residues: 718 sheet: 1.19 (0.77), residues: 44 loop : -1.94 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.005 0.001 HIS A 619 PHE 0.007 0.001 PHE A 615 TYR 0.009 0.001 TYR A 589 ARG 0.001 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.878 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1330 time to fit residues: 15.8794 Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.117598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.087785 restraints weight = 10366.897| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.59 r_work: 0.2708 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8718 Z= 0.159 Angle : 0.481 7.390 11890 Z= 0.254 Chirality : 0.039 0.126 1400 Planarity : 0.004 0.039 1438 Dihedral : 11.535 101.751 1326 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.76 % Allowed : 11.84 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.27), residues: 1060 helix: 0.53 (0.21), residues: 716 sheet: 1.41 (0.80), residues: 44 loop : -1.86 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.008 0.001 PHE A 615 TYR 0.008 0.001 TYR B 180 ARG 0.001 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.898 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.1311 time to fit residues: 15.6627 Evaluate side-chains 72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.118366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.088504 restraints weight = 10271.323| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.59 r_work: 0.2729 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8718 Z= 0.145 Angle : 0.470 7.387 11890 Z= 0.248 Chirality : 0.038 0.121 1400 Planarity : 0.004 0.039 1438 Dihedral : 11.081 98.087 1326 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.76 % Allowed : 11.84 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.27), residues: 1060 helix: 0.76 (0.21), residues: 710 sheet: 1.55 (0.81), residues: 44 loop : -1.82 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.003 0.001 HIS B 130 PHE 0.007 0.001 PHE A 615 TYR 0.008 0.001 TYR B 180 ARG 0.000 0.000 ARG B 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.945 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.1306 time to fit residues: 15.7376 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.119463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.089623 restraints weight = 10468.270| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.61 r_work: 0.2745 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8718 Z= 0.130 Angle : 0.460 7.370 11890 Z= 0.242 Chirality : 0.038 0.121 1400 Planarity : 0.004 0.039 1438 Dihedral : 10.700 94.535 1326 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.63 % Allowed : 11.96 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.28), residues: 1060 helix: 0.95 (0.21), residues: 710 sheet: 1.56 (0.83), residues: 44 loop : -1.73 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.003 0.001 HIS A 130 PHE 0.007 0.001 PHE A 615 TYR 0.008 0.001 TYR B 180 ARG 0.001 0.000 ARG A 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4019.17 seconds wall clock time: 72 minutes 3.40 seconds (4323.40 seconds total)