Starting phenix.real_space_refine on Sat Apr 6 23:39:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5b_24185/04_2024/7n5b_24185_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5b_24185/04_2024/7n5b_24185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5b_24185/04_2024/7n5b_24185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5b_24185/04_2024/7n5b_24185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5b_24185/04_2024/7n5b_24185_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5b_24185/04_2024/7n5b_24185_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.019 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5802 2.51 5 N 1566 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9122 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4528 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 12, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 4528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4528 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 12, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.93, per 1000 atoms: 0.54 Number of scatterers: 9122 At special positions: 0 Unit cell: (84.645, 76.095, 137.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 34 16.00 P 4 15.00 Mg 2 11.99 O 1712 8.00 N 1566 7.00 C 5802 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 - 3.50 Amino acid : False - 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: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 4 sheets defined 65.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.515A pdb=" N TYR A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 173 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 196 through 244 removed outlier: 3.575A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 295 removed outlier: 4.190A pdb=" N ASN A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 302 through 354 removed outlier: 4.113A pdb=" N LYS A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N THR A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 408 removed outlier: 3.509A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 457 removed outlier: 3.651A pdb=" N VAL A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.583A pdb=" N VAL A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 518 through 525 removed outlier: 4.170A pdb=" N LEU A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.683A pdb=" N SER A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 removed outlier: 4.641A pdb=" N GLY A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.521A pdb=" N ARG A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 618 through 632 Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.505A pdb=" N ALA A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.515A pdb=" N TYR B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 173 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 196 through 244 removed outlier: 3.574A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 4.189A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 302 through 354 removed outlier: 4.113A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N THR B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 408 removed outlier: 3.508A pdb=" N THR B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 457 removed outlier: 3.651A pdb=" N VAL B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.583A pdb=" N VAL B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N MET B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 454 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 518 through 525 removed outlier: 4.170A pdb=" N LEU B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 554 removed outlier: 3.682A pdb=" N SER B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 removed outlier: 4.641A pdb=" N GLY B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.522A pdb=" N ARG B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 611 through 613 No H-bonds generated for 'chain 'B' and resid 611 through 613' Processing helix chain 'B' and resid 618 through 632 Processing helix chain 'B' and resid 648 through 663 removed outlier: 3.504A pdb=" N ALA B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 663 " --> pdb=" O LYS B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 697 through 703 Processing helix chain 'B' and resid 706 through 715 Processing sheet with id= A, first strand: chain 'A' and resid 479 through 482 Processing sheet with id= B, first strand: chain 'A' and resid 690 through 695 removed outlier: 6.715A pdb=" N VAL A 685 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN A 694 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 683 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 682 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER A 667 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE A 510 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 669 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 637 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE A 670 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS A 639 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 479 through 482 Processing sheet with id= D, first strand: chain 'B' and resid 690 through 695 removed outlier: 6.714A pdb=" N VAL B 685 " --> pdb=" O VAL B 692 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN B 694 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 683 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 682 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 667 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ILE B 510 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE B 669 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 637 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 670 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS B 639 " --> pdb=" O ILE B 670 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1644 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: 2.65 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 3010 1.36 - 1.50: 2337 1.50 - 1.64: 3863 1.64 - 1.77: 0 1.77 - 1.91: 70 Bond restraints: 9280 Sorted by residual: bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" CA LYS B 470 " pdb=" CB LYS B 470 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.51e-02 4.39e+03 7.00e-01 bond pdb=" CA LYS A 470 " pdb=" CB LYS A 470 " ideal model delta sigma weight residual 1.526 1.539 -0.012 1.51e-02 4.39e+03 6.79e-01 bond pdb=" CG GLU B 458 " pdb=" CD GLU B 458 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.52e-01 ... (remaining 9275 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.31: 202 107.31 - 114.43: 5559 114.43 - 121.55: 4910 121.55 - 128.68: 1835 128.68 - 135.80: 50 Bond angle restraints: 12556 Sorted by residual: angle pdb=" CB MET B 453 " pdb=" CG MET B 453 " pdb=" SD MET B 453 " ideal model delta sigma weight residual 112.70 105.61 7.09 3.00e+00 1.11e-01 5.59e+00 angle pdb=" CB MET A 453 " pdb=" CG MET A 453 " pdb=" SD MET A 453 " ideal model delta sigma weight residual 112.70 105.62 7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" CB GLU B 458 " pdb=" CG GLU B 458 " pdb=" CD GLU B 458 " ideal model delta sigma weight residual 112.60 116.34 -3.74 1.70e+00 3.46e-01 4.85e+00 angle pdb=" CB GLU A 458 " pdb=" CG GLU A 458 " pdb=" CD GLU A 458 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.70e+00 3.46e-01 4.77e+00 angle pdb=" CA LYS B 297 " pdb=" CB LYS B 297 " pdb=" CG LYS B 297 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.58e+00 ... (remaining 12551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 5122 21.16 - 42.32: 364 42.32 - 63.48: 38 63.48 - 84.64: 8 84.64 - 105.80: 8 Dihedral angle restraints: 5540 sinusoidal: 2184 harmonic: 3356 Sorted by residual: dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 45.80 -105.80 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 45.73 -105.73 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 -150.08 90.08 1 2.00e+01 2.50e-03 2.40e+01 ... (remaining 5537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1069 0.031 - 0.063: 268 0.063 - 0.094: 87 0.094 - 0.126: 31 0.126 - 0.157: 3 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CB ILE B 538 " pdb=" CA ILE B 538 " pdb=" CG1 ILE B 538 " pdb=" CG2 ILE B 538 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CB ILE A 538 " pdb=" CA ILE A 538 " pdb=" CG1 ILE A 538 " pdb=" CG2 ILE A 538 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE B 683 " pdb=" N ILE B 683 " pdb=" C ILE B 683 " pdb=" CB ILE B 683 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1455 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 239 " 0.010 2.00e-02 2.50e+03 7.39e-03 9.57e-01 pdb=" CG PHE A 239 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 239 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 239 " -0.010 2.00e-02 2.50e+03 7.32e-03 9.37e-01 pdb=" CG PHE B 239 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 239 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 239 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 239 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 510 " -0.004 2.00e-02 2.50e+03 8.48e-03 7.19e-01 pdb=" C ILE B 510 " 0.015 2.00e-02 2.50e+03 pdb=" O ILE B 510 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 511 " -0.005 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 6749 3.10 - 3.70: 13477 3.70 - 4.30: 18518 4.30 - 4.90: 29887 Nonbonded interactions: 68669 Sorted by model distance: nonbonded pdb=" V VO4 A 802 " pdb="MG MG A 803 " model vdw 1.903 2.180 nonbonded pdb=" V VO4 B 802 " pdb="MG MG B 803 " model vdw 1.903 2.180 nonbonded pdb=" O1 VO4 A 802 " pdb="MG MG A 803 " model vdw 2.115 2.170 nonbonded pdb=" O1 VO4 B 802 " pdb="MG MG B 803 " model vdw 2.116 2.170 nonbonded pdb=" O2 VO4 A 802 " pdb="MG MG A 803 " model vdw 2.127 2.170 ... (remaining 68664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 6.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.350 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.002 0.024 9280 Z= 0.109 Angle : 0.482 7.092 12556 Z= 0.240 Chirality : 0.035 0.157 1458 Planarity : 0.002 0.024 1584 Dihedral : 14.243 105.795 3372 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.20 % Allowed : 0.41 % Favored : 99.39 % 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: 2.06 (0.24), residues: 1152 helix: 2.03 (0.18), residues: 754 sheet: 2.83 (0.61), residues: 74 loop : -0.60 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 323 HIS 0.001 0.000 HIS B 243 PHE 0.016 0.001 PHE A 239 TYR 0.014 0.001 TYR B 205 ARG 0.006 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.952 Fit side-chains REVERT: A 276 MET cc_start: 0.7701 (ttp) cc_final: 0.7463 (tmm) REVERT: A 498 ILE cc_start: 0.7578 (mt) cc_final: 0.7334 (mm) REVERT: B 498 ILE cc_start: 0.7584 (mt) cc_final: 0.7323 (mm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.1630 time to fit residues: 30.5018 Evaluate side-chains 94 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN B 159 GLN B 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9280 Z= 0.220 Angle : 0.574 8.294 12556 Z= 0.293 Chirality : 0.038 0.122 1458 Planarity : 0.003 0.016 1584 Dihedral : 6.807 120.878 1278 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.74 % Allowed : 7.67 % Favored : 90.59 % 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: 2.62 (0.24), residues: 1152 helix: 2.64 (0.19), residues: 752 sheet: 2.72 (0.60), residues: 74 loop : -0.78 (0.29), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.005 0.001 HIS B 250 PHE 0.013 0.002 PHE A 149 TYR 0.012 0.001 TYR B 440 ARG 0.004 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.925 Fit side-chains REVERT: A 156 LEU cc_start: 0.8501 (tt) cc_final: 0.8197 (tt) REVERT: A 646 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 646 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8075 (mp) outliers start: 17 outliers final: 5 residues processed: 125 average time/residue: 0.1845 time to fit residues: 33.8735 Evaluate side-chains 96 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 114 optimal weight: 0.2980 chunk 93 optimal weight: 0.1980 chunk 104 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 357 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9280 Z= 0.140 Angle : 0.501 7.832 12556 Z= 0.252 Chirality : 0.036 0.133 1458 Planarity : 0.002 0.024 1584 Dihedral : 6.867 127.349 1278 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.33 % Allowed : 12.27 % Favored : 86.40 % 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: 2.77 (0.25), residues: 1152 helix: 2.83 (0.19), residues: 742 sheet: 2.51 (0.61), residues: 74 loop : -0.74 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 170 HIS 0.002 0.001 HIS B 243 PHE 0.009 0.001 PHE B 271 TYR 0.010 0.001 TYR A 205 ARG 0.004 0.000 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.945 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 102 average time/residue: 0.1712 time to fit residues: 26.6053 Evaluate side-chains 89 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9280 Z= 0.149 Angle : 0.508 7.793 12556 Z= 0.254 Chirality : 0.037 0.204 1458 Planarity : 0.002 0.023 1584 Dihedral : 6.762 125.654 1278 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.33 % Allowed : 13.80 % Favored : 84.87 % 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: 2.77 (0.25), residues: 1152 helix: 2.85 (0.19), residues: 744 sheet: 2.35 (0.61), residues: 74 loop : -0.77 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 132 HIS 0.003 0.001 HIS B 250 PHE 0.011 0.001 PHE B 271 TYR 0.007 0.001 TYR B 249 ARG 0.005 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.038 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 99 average time/residue: 0.1602 time to fit residues: 25.0695 Evaluate side-chains 90 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 629 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS B 485 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9280 Z= 0.158 Angle : 0.510 8.005 12556 Z= 0.254 Chirality : 0.036 0.128 1458 Planarity : 0.002 0.022 1584 Dihedral : 6.762 127.667 1278 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.64 % Allowed : 14.83 % Favored : 83.54 % 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: 2.77 (0.25), residues: 1152 helix: 2.86 (0.19), residues: 744 sheet: 2.16 (0.60), residues: 74 loop : -0.75 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 132 HIS 0.003 0.001 HIS B 485 PHE 0.010 0.001 PHE B 271 TYR 0.009 0.001 TYR B 249 ARG 0.005 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.142 Fit side-chains REVERT: A 646 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8125 (mp) REVERT: B 156 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 450 MET cc_start: 0.7412 (tpp) cc_final: 0.7042 (tpp) REVERT: B 646 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8071 (mp) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.1632 time to fit residues: 26.2447 Evaluate side-chains 93 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 0.0040 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9280 Z= 0.137 Angle : 0.502 7.389 12556 Z= 0.248 Chirality : 0.036 0.131 1458 Planarity : 0.002 0.022 1584 Dihedral : 6.709 127.995 1278 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.82 % Allowed : 16.97 % Favored : 82.21 % 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: 2.80 (0.25), residues: 1152 helix: 2.89 (0.19), residues: 744 sheet: 2.13 (0.59), residues: 74 loop : -0.75 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 132 HIS 0.002 0.001 HIS B 250 PHE 0.012 0.001 PHE B 149 TYR 0.007 0.001 TYR A 205 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.986 Fit side-chains REVERT: A 450 MET cc_start: 0.7336 (tpp) cc_final: 0.6982 (tpp) REVERT: B 156 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8397 (tt) REVERT: B 217 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7310 (tm-30) REVERT: B 450 MET cc_start: 0.7388 (tpp) cc_final: 0.7006 (tpp) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.1655 time to fit residues: 24.6580 Evaluate side-chains 90 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 567 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9280 Z= 0.139 Angle : 0.499 7.702 12556 Z= 0.246 Chirality : 0.036 0.128 1458 Planarity : 0.002 0.021 1584 Dihedral : 6.601 125.144 1278 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.43 % Allowed : 16.97 % Favored : 81.60 % 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: 2.84 (0.25), residues: 1152 helix: 2.92 (0.19), residues: 744 sheet: 2.15 (0.60), residues: 74 loop : -0.74 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 132 HIS 0.002 0.001 HIS A 243 PHE 0.016 0.001 PHE A 271 TYR 0.007 0.001 TYR B 249 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.934 Fit side-chains REVERT: A 450 MET cc_start: 0.7409 (tpp) cc_final: 0.6960 (tpp) REVERT: A 646 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 217 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7315 (tm-30) REVERT: B 450 MET cc_start: 0.7504 (tpp) cc_final: 0.7085 (tpp) REVERT: B 646 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8081 (mp) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.1485 time to fit residues: 23.8794 Evaluate side-chains 95 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9280 Z= 0.153 Angle : 0.516 7.990 12556 Z= 0.253 Chirality : 0.036 0.129 1458 Planarity : 0.002 0.021 1584 Dihedral : 6.525 122.851 1278 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.12 % Allowed : 17.79 % Favored : 81.08 % 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: 2.81 (0.25), residues: 1152 helix: 2.90 (0.19), residues: 744 sheet: 2.14 (0.57), residues: 74 loop : -0.75 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 170 HIS 0.002 0.001 HIS A 241 PHE 0.012 0.001 PHE B 435 TYR 0.006 0.001 TYR B 249 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.098 Fit side-chains REVERT: A 450 MET cc_start: 0.7433 (tpp) cc_final: 0.7073 (tpp) REVERT: A 646 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8097 (mp) REVERT: B 217 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7368 (tm-30) REVERT: B 450 MET cc_start: 0.7494 (tpp) cc_final: 0.7210 (tpp) REVERT: B 646 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (mp) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.1538 time to fit residues: 23.1571 Evaluate side-chains 96 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9280 Z= 0.183 Angle : 0.537 8.186 12556 Z= 0.266 Chirality : 0.037 0.137 1458 Planarity : 0.002 0.021 1584 Dihedral : 6.479 118.869 1278 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.64 % Allowed : 17.89 % Favored : 80.47 % 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 (0.25), residues: 1152 helix: 2.88 (0.19), residues: 740 sheet: 2.04 (0.58), residues: 74 loop : -0.81 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 170 HIS 0.004 0.001 HIS B 250 PHE 0.012 0.001 PHE B 435 TYR 0.009 0.001 TYR B 249 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.945 Fit side-chains REVERT: A 450 MET cc_start: 0.7504 (tpp) cc_final: 0.7103 (tpp) REVERT: A 646 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 201 VAL cc_start: 0.7528 (m) cc_final: 0.7307 (p) REVERT: B 450 MET cc_start: 0.7566 (tpp) cc_final: 0.7285 (tpp) REVERT: B 646 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8096 (mp) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.1520 time to fit residues: 23.5778 Evaluate side-chains 95 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 106 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9280 Z= 0.157 Angle : 0.536 9.400 12556 Z= 0.266 Chirality : 0.037 0.135 1458 Planarity : 0.002 0.021 1584 Dihedral : 6.449 116.876 1278 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.43 % Allowed : 18.40 % Favored : 80.16 % 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: 2.70 (0.25), residues: 1152 helix: 2.85 (0.19), residues: 738 sheet: 1.97 (0.58), residues: 74 loop : -0.76 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 170 HIS 0.002 0.001 HIS A 250 PHE 0.015 0.001 PHE A 215 TYR 0.006 0.001 TYR B 249 ARG 0.003 0.000 ARG A 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.216 Fit side-chains REVERT: A 450 MET cc_start: 0.7471 (tpp) cc_final: 0.7079 (tpp) REVERT: A 646 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 201 VAL cc_start: 0.7563 (m) cc_final: 0.7335 (p) REVERT: B 450 MET cc_start: 0.7546 (tpp) cc_final: 0.7276 (tpp) REVERT: B 646 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8041 (mp) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.1408 time to fit residues: 22.2756 Evaluate side-chains 97 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.149240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111234 restraints weight = 14283.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114395 restraints weight = 8535.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116624 restraints weight = 6111.667| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9280 Z= 0.250 Angle : 0.602 9.671 12556 Z= 0.303 Chirality : 0.039 0.138 1458 Planarity : 0.003 0.022 1584 Dihedral : 6.502 107.500 1278 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.53 % Allowed : 18.71 % Favored : 79.75 % 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: 2.41 (0.25), residues: 1152 helix: 2.63 (0.19), residues: 736 sheet: 1.89 (0.58), residues: 74 loop : -0.91 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 323 HIS 0.006 0.002 HIS A 250 PHE 0.014 0.001 PHE A 215 TYR 0.010 0.001 TYR B 249 ARG 0.003 0.000 ARG B 665 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.06 seconds wall clock time: 31 minutes 43.50 seconds (1903.50 seconds total)