Starting phenix.real_space_refine on Thu Jul 2 16:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yr3_39534/07_2026/8yr3_39534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yr3_39534/07_2026/8yr3_39534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yr3_39534/07_2026/8yr3_39534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yr3_39534/07_2026/8yr3_39534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yr3_39534/07_2026/8yr3_39534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yr3_39534/07_2026/8yr3_39534.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 Cd 1 9.23 5 S 36 5.16 5 C 5978 2.51 5 N 1616 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9319 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4639 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 573} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4639 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 573} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.20 Number of scatterers: 9319 At special positions: 0 Unit cell: (72.21, 101.26, 138.61, 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) Cd 1 47.96 S 36 16.00 O 1688 8.00 N 1616 7.00 C 5978 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: 0.69 Conformation dependent library (CDL) restraints added in 275.9 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 71.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 241 through 254 removed outlier: 4.187A pdb=" N LYS A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 295 Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 324 through 355 removed outlier: 4.583A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.956A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 364 " --> pdb=" O TRP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 391 removed outlier: 3.715A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 409 removed outlier: 3.619A pdb=" N PHE A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 455 removed outlier: 3.702A pdb=" N VAL A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 468 through 522 removed outlier: 3.726A pdb=" N GLU A 522 " --> pdb=" O TYR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 570 removed outlier: 4.203A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 3.737A pdb=" N TYR A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.757A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.752A pdb=" N VAL A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 758 through 774 Processing helix chain 'A' and resid 785 through 790 removed outlier: 4.643A pdb=" N ASN A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 removed outlier: 4.259A pdb=" N GLY A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.765A pdb=" N GLN A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.879A pdb=" N LYS B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 295 removed outlier: 3.586A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 298 through 316 Processing helix chain 'B' and resid 324 through 355 removed outlier: 4.588A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 removed outlier: 3.862A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 391 removed outlier: 3.730A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.576A pdb=" N PHE B 409 " --> pdb=" O PHE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 455 removed outlier: 4.173A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 468 through 522 removed outlier: 3.736A pdb=" N GLY B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 522 " --> pdb=" O TYR B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 542 removed outlier: 4.329A pdb=" N TYR B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 546 through 570 removed outlier: 3.502A pdb=" N PHE B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 655 through 657 No H-bonds generated for 'chain 'B' and resid 655 through 657' Processing helix chain 'B' and resid 658 through 665 removed outlier: 3.932A pdb=" N LEU B 662 " --> pdb=" O THR B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 686 Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.845A pdb=" N VAL B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 712 removed outlier: 3.737A pdb=" N PHE B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.837A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 744 Processing helix chain 'B' and resid 758 through 774 Processing helix chain 'B' and resid 785 through 790 removed outlier: 4.701A pdb=" N ASN B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 815 removed outlier: 3.505A pdb=" N LEU B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.773A pdb=" N GLN B 826 " --> pdb=" O TRP B 822 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 609 removed outlier: 5.446A pdb=" N VAL A 595 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 590 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 613 " --> pdb=" O ILE A 590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 609 removed outlier: 5.446A pdb=" N VAL A 595 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE A 592 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ARG A 648 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN A 594 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS A 646 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 667 removed outlier: 6.187A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU A 795 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 620 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 606 through 609 removed outlier: 5.273A pdb=" N VAL B 595 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE B 592 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ARG B 648 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASN B 594 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N CYS B 646 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 666 through 667 removed outlier: 6.316A pdb=" N ILE B 748 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL B 781 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1818 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: 1.28 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1505 1.30 - 1.43: 2531 1.43 - 1.56: 5400 1.56 - 1.69: 2 1.69 - 1.82: 58 Bond restraints: 9496 Sorted by residual: bond pdb=" C MET A 542 " pdb=" O MET A 542 " ideal model delta sigma weight residual 1.238 1.398 -0.160 1.28e-02 6.10e+03 1.57e+02 bond pdb=" C GLN A 539 " pdb=" O GLN A 539 " ideal model delta sigma weight residual 1.236 1.369 -0.132 1.15e-02 7.56e+03 1.32e+02 bond pdb=" C ASN A 545 " pdb=" O ASN A 545 " ideal model delta sigma weight residual 1.236 1.355 -0.119 1.15e-02 7.56e+03 1.06e+02 bond pdb=" CA PHE A 547 " pdb=" C PHE A 547 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.24e-02 6.50e+03 7.83e+01 bond pdb=" N THR A 549 " pdb=" CA THR A 549 " ideal model delta sigma weight residual 1.459 1.543 -0.084 1.16e-02 7.43e+03 5.27e+01 ... (remaining 9491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 12710 4.15 - 8.29: 140 8.29 - 12.44: 21 12.44 - 16.59: 1 16.59 - 20.74: 2 Bond angle restraints: 12874 Sorted by residual: angle pdb=" C MET A 542 " pdb=" N PRO A 543 " pdb=" CA PRO A 543 " ideal model delta sigma weight residual 119.05 98.74 20.31 1.11e+00 8.12e-01 3.35e+02 angle pdb=" C ASN A 545 " pdb=" N TRP A 546 " pdb=" CA TRP A 546 " ideal model delta sigma weight residual 120.99 100.25 20.74 1.86e+00 2.89e-01 1.24e+02 angle pdb=" N LEU B 507 " pdb=" CA LEU B 507 " pdb=" C LEU B 507 " ideal model delta sigma weight residual 111.33 99.40 11.93 1.21e+00 6.83e-01 9.72e+01 angle pdb=" CA ASN A 545 " pdb=" C ASN A 545 " pdb=" O ASN A 545 " ideal model delta sigma weight residual 121.00 130.26 -9.26 1.05e+00 9.07e-01 7.77e+01 angle pdb=" N SER B 493 " pdb=" CA SER B 493 " pdb=" C SER B 493 " ideal model delta sigma weight residual 111.82 102.11 9.71 1.16e+00 7.43e-01 7.00e+01 ... (remaining 12869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4702 17.30 - 34.60: 669 34.60 - 51.90: 201 51.90 - 69.20: 34 69.20 - 86.50: 14 Dihedral angle restraints: 5620 sinusoidal: 2246 harmonic: 3374 Sorted by residual: dihedral pdb=" N THR A 549 " pdb=" C THR A 549 " pdb=" CA THR A 549 " pdb=" CB THR A 549 " ideal model delta harmonic sigma weight residual 123.40 133.20 -9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C PHE A 547 " pdb=" N PHE A 547 " pdb=" CA PHE A 547 " pdb=" CB PHE A 547 " ideal model delta harmonic sigma weight residual -122.60 -113.61 -8.99 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CA LYS A 575 " pdb=" C LYS A 575 " pdb=" N ASP A 576 " pdb=" CA ASP A 576 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1234 0.061 - 0.123: 207 0.123 - 0.184: 31 0.184 - 0.245: 10 0.245 - 0.307: 4 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CG LEU A 635 " pdb=" CB LEU A 635 " pdb=" CD1 LEU A 635 " pdb=" CD2 LEU A 635 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA MET A 553 " pdb=" N MET A 553 " pdb=" C MET A 553 " pdb=" CB MET A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR B 432 " pdb=" N THR B 432 " pdb=" C THR B 432 " pdb=" CB THR B 432 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1483 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH B 901 " 0.082 2.00e-02 2.50e+03 2.47e-01 7.63e+02 pdb=" CA2 GSH B 901 " -0.193 2.00e-02 2.50e+03 pdb=" CA3 GSH B 901 " -0.297 2.00e-02 2.50e+03 pdb=" N3 GSH B 901 " 0.416 2.00e-02 2.50e+03 pdb=" O2 GSH B 901 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 901 " -0.068 2.00e-02 2.50e+03 2.01e-01 5.04e+02 pdb=" CA2 GSH A 901 " 0.172 2.00e-02 2.50e+03 pdb=" CA3 GSH A 901 " 0.243 2.00e-02 2.50e+03 pdb=" N3 GSH A 901 " -0.329 2.00e-02 2.50e+03 pdb=" O2 GSH A 901 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GSH B 901 " 0.175 2.00e-02 2.50e+03 1.99e-01 4.93e+02 pdb=" CD1 GSH B 901 " -0.075 2.00e-02 2.50e+03 pdb=" OE1 GSH B 901 " -0.027 2.00e-02 2.50e+03 pdb=" CA2 GSH B 901 " 0.244 2.00e-02 2.50e+03 pdb=" N2 GSH B 901 " -0.317 2.00e-02 2.50e+03 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2008 2.77 - 3.30: 9242 3.30 - 3.83: 15198 3.83 - 4.37: 15843 4.37 - 4.90: 27608 Nonbonded interactions: 69899 Sorted by model distance: nonbonded pdb=" O THR A 428 " pdb=" OG1 THR A 432 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP A 678 " pdb=" N THR A 679 " model vdw 2.240 3.120 nonbonded pdb=" O THR B 320 " pdb=" OG1 THR B 320 " model vdw 2.247 3.040 nonbonded pdb=" ND2 ASN A 279 " pdb=" OD2 ASP A 397 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS B 245 " pdb=" OE1 GLU B 562 " model vdw 2.258 3.120 ... (remaining 69894 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 240 through 901) 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.050 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 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 : 0.008 0.160 9496 Z= 0.577 Angle : 1.036 20.736 12874 Z= 0.650 Chirality : 0.051 0.307 1486 Planarity : 0.011 0.247 1632 Dihedral : 17.815 86.505 3460 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.16 % Rotamer: Outliers : 1.31 % Allowed : 29.29 % Favored : 69.39 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1170 helix: 1.26 (0.19), residues: 756 sheet: 1.01 (0.68), residues: 60 loop : -2.47 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 552 TYR 0.020 0.002 TYR A 550 PHE 0.021 0.002 PHE A 585 TRP 0.042 0.003 TRP A 822 HIS 0.004 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.58 ( 9496) covalent geometry : angle 1.03580 / 0.65 (12874) hydrogen bonds : bond 0.14745 / 10.06 ( 613) hydrogen bonds : angle 6.03120 / 4.57 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 ILE cc_start: 0.9160 (mm) cc_final: 0.8940 (mm) REVERT: A 542 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.9097 (mpp) REVERT: A 543 PRO cc_start: 0.9162 (OUTLIER) cc_final: 0.8945 (Cg_exo) REVERT: A 566 ASP cc_start: 0.9598 (t0) cc_final: 0.9368 (t0) REVERT: A 706 HIS cc_start: 0.9105 (t70) cc_final: 0.8094 (t70) REVERT: B 330 ARG cc_start: 0.9036 (tmm160) cc_final: 0.8782 (ttp80) REVERT: B 416 ILE cc_start: 0.9143 (mm) cc_final: 0.8922 (mm) REVERT: B 455 ASP cc_start: 0.9281 (m-30) cc_final: 0.8736 (p0) REVERT: B 566 ASP cc_start: 0.9511 (t0) cc_final: 0.9192 (t0) REVERT: B 586 GLN cc_start: 0.7983 (mm110) cc_final: 0.7496 (mm110) REVERT: B 668 VAL cc_start: 0.9565 (t) cc_final: 0.9255 (m) REVERT: B 710 MET cc_start: 0.9308 (mmt) cc_final: 0.9027 (mpp) REVERT: B 749 LEU cc_start: 0.9532 (mm) cc_final: 0.9258 (mm) outliers start: 13 outliers final: 7 residues processed: 156 average time/residue: 0.0729 time to fit residues: 16.5226 Evaluate side-chains 103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 PRO Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 505 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 GLN A 719 GLN A 733 GLN B 719 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.083310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059606 restraints weight = 37258.981| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.42 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9496 Z= 0.154 Angle : 0.635 10.730 12874 Z= 0.327 Chirality : 0.041 0.256 1486 Planarity : 0.004 0.036 1632 Dihedral : 7.667 53.881 1352 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.34 % Allowed : 27.58 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1170 helix: 1.80 (0.19), residues: 750 sheet: 0.88 (0.64), residues: 62 loop : -2.25 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.019 0.001 TYR A 550 PHE 0.012 0.001 PHE A 325 TRP 0.037 0.002 TRP A 434 HIS 0.005 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9496) covalent geometry : angle 0.63540 / 0.33 (12874) hydrogen bonds : bond 0.07049 / 4.71 ( 613) hydrogen bonds : angle 4.33229 / 3.26 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9322 (p) REVERT: B 374 ASP cc_start: 0.9250 (m-30) cc_final: 0.8959 (t0) REVERT: B 455 ASP cc_start: 0.9161 (m-30) cc_final: 0.8627 (p0) REVERT: B 562 GLU cc_start: 0.9564 (tp30) cc_final: 0.9149 (mm-30) REVERT: B 566 ASP cc_start: 0.9654 (t0) cc_final: 0.9430 (t0) REVERT: B 749 LEU cc_start: 0.9606 (mm) cc_final: 0.9306 (mm) outliers start: 43 outliers final: 17 residues processed: 143 average time/residue: 0.0583 time to fit residues: 13.3907 Evaluate side-chains 107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 505 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 677 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060560 restraints weight = 38612.618| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 5.48 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9496 Z= 0.149 Angle : 0.602 12.491 12874 Z= 0.308 Chirality : 0.040 0.223 1486 Planarity : 0.004 0.040 1632 Dihedral : 7.028 57.647 1341 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.23 % Allowed : 28.59 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1170 helix: 2.15 (0.19), residues: 750 sheet: 0.72 (0.62), residues: 62 loop : -2.17 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 634 TYR 0.017 0.001 TYR B 686 PHE 0.011 0.001 PHE B 676 TRP 0.042 0.002 TRP A 822 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 9496) covalent geometry : angle 0.60192 / 0.31 (12874) hydrogen bonds : bond 0.06522 / 4.35 ( 613) hydrogen bonds : angle 4.18077 / 3.14 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9313 (mp) REVERT: B 455 ASP cc_start: 0.9159 (m-30) cc_final: 0.8608 (p0) REVERT: B 566 ASP cc_start: 0.9653 (t0) cc_final: 0.9430 (t0) outliers start: 32 outliers final: 18 residues processed: 128 average time/residue: 0.0526 time to fit residues: 10.6310 Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 505 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.076866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054785 restraints weight = 38211.203| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.24 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9496 Z= 0.195 Angle : 0.615 10.970 12874 Z= 0.322 Chirality : 0.040 0.200 1486 Planarity : 0.004 0.042 1632 Dihedral : 6.640 51.558 1340 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.64 % Allowed : 28.99 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1170 helix: 2.09 (0.19), residues: 756 sheet: 0.24 (0.61), residues: 62 loop : -2.07 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 584 TYR 0.014 0.001 TYR B 465 PHE 0.016 0.001 PHE A 325 TRP 0.043 0.002 TRP A 822 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 9496) covalent geometry : angle 0.61519 / 0.32 (12874) hydrogen bonds : bond 0.06826 / 4.54 ( 613) hydrogen bonds : angle 4.31659 / 3.26 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9285 (mp) REVERT: A 822 TRP cc_start: 0.8650 (p-90) cc_final: 0.8368 (p-90) REVERT: A 824 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 374 ASP cc_start: 0.9272 (m-30) cc_final: 0.9008 (t0) REVERT: B 455 ASP cc_start: 0.9171 (m-30) cc_final: 0.8722 (p0) REVERT: B 566 ASP cc_start: 0.9700 (t0) cc_final: 0.9497 (t0) REVERT: B 635 LEU cc_start: 0.9667 (mm) cc_final: 0.9466 (mm) outliers start: 36 outliers final: 23 residues processed: 121 average time/residue: 0.0702 time to fit residues: 13.2415 Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 811 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 ASN B 733 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.078026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056023 restraints weight = 37439.257| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.20 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9496 Z= 0.148 Angle : 0.595 12.559 12874 Z= 0.304 Chirality : 0.039 0.210 1486 Planarity : 0.003 0.043 1632 Dihedral : 6.336 49.053 1340 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.43 % Allowed : 29.90 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1170 helix: 2.21 (0.19), residues: 756 sheet: 0.06 (0.61), residues: 62 loop : -2.06 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.012 0.001 TYR B 536 PHE 0.018 0.001 PHE A 418 TRP 0.026 0.002 TRP A 822 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 9496) covalent geometry : angle 0.59454 / 0.30 (12874) hydrogen bonds : bond 0.06508 / 4.31 ( 613) hydrogen bonds : angle 4.14854 / 3.12 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 TRP cc_start: 0.8671 (p-90) cc_final: 0.8317 (p-90) REVERT: B 455 ASP cc_start: 0.9178 (m-30) cc_final: 0.8740 (p0) REVERT: B 614 MET cc_start: 0.9090 (tmm) cc_final: 0.8890 (tmm) REVERT: B 635 LEU cc_start: 0.9663 (mm) cc_final: 0.9402 (mm) outliers start: 34 outliers final: 22 residues processed: 119 average time/residue: 0.0700 time to fit residues: 13.2453 Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 811 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.076921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055043 restraints weight = 37661.407| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.19 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9496 Z= 0.165 Angle : 0.587 11.092 12874 Z= 0.304 Chirality : 0.039 0.221 1486 Planarity : 0.003 0.044 1632 Dihedral : 6.136 52.765 1340 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.43 % Allowed : 30.20 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1170 helix: 2.21 (0.19), residues: 756 sheet: 0.01 (0.61), residues: 62 loop : -2.00 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.013 0.001 TYR B 536 PHE 0.014 0.001 PHE A 325 TRP 0.023 0.002 TRP A 822 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 9496) covalent geometry : angle 0.58700 / 0.30 (12874) hydrogen bonds : bond 0.06420 / 4.27 ( 613) hydrogen bonds : angle 4.18309 / 3.14 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 TRP cc_start: 0.8695 (p-90) cc_final: 0.8344 (p-90) REVERT: B 455 ASP cc_start: 0.9194 (m-30) cc_final: 0.8836 (p0) REVERT: B 635 LEU cc_start: 0.9671 (mm) cc_final: 0.9425 (mm) REVERT: B 710 MET cc_start: 0.9531 (mmt) cc_final: 0.9221 (mpp) outliers start: 34 outliers final: 26 residues processed: 118 average time/residue: 0.0680 time to fit residues: 12.8514 Evaluate side-chains 108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 chunk 91 optimal weight: 0.4980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.078685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056306 restraints weight = 38096.699| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 5.32 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9496 Z= 0.129 Angle : 0.583 13.268 12874 Z= 0.293 Chirality : 0.039 0.228 1486 Planarity : 0.003 0.042 1632 Dihedral : 5.887 51.399 1338 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.42 % Allowed : 31.11 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1170 helix: 2.33 (0.19), residues: 756 sheet: 0.04 (0.62), residues: 62 loop : -1.97 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.010 0.001 TYR B 536 PHE 0.021 0.001 PHE A 418 TRP 0.023 0.002 TRP A 822 HIS 0.002 0.001 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 9496) covalent geometry : angle 0.58316 / 0.29 (12874) hydrogen bonds : bond 0.05828 / 3.85 ( 613) hydrogen bonds : angle 3.97345 / 2.98 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.8947 (pp30) REVERT: A 355 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.8897 (tp30) REVERT: A 822 TRP cc_start: 0.8732 (p-90) cc_final: 0.8276 (p-90) REVERT: B 455 ASP cc_start: 0.9113 (m-30) cc_final: 0.8808 (p0) REVERT: B 635 LEU cc_start: 0.9701 (mm) cc_final: 0.9411 (mm) REVERT: B 710 MET cc_start: 0.9545 (mmt) cc_final: 0.9273 (mpp) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.0635 time to fit residues: 12.3378 Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.076515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054650 restraints weight = 37623.181| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 5.14 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9496 Z= 0.168 Angle : 0.610 12.730 12874 Z= 0.310 Chirality : 0.040 0.235 1486 Planarity : 0.003 0.039 1632 Dihedral : 5.938 57.687 1338 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.53 % Allowed : 31.62 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1170 helix: 2.26 (0.19), residues: 756 sheet: -0.04 (0.61), residues: 62 loop : -1.97 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.012 0.001 TYR B 536 PHE 0.015 0.001 PHE A 325 TRP 0.021 0.001 TRP A 822 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9496) covalent geometry : angle 0.60985 / 0.31 (12874) hydrogen bonds : bond 0.06146 / 4.07 ( 613) hydrogen bonds : angle 4.11514 / 3.10 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8900 (tp30) REVERT: A 822 TRP cc_start: 0.8780 (p-90) cc_final: 0.8379 (p-90) REVERT: B 374 ASP cc_start: 0.9278 (m-30) cc_final: 0.9034 (t0) REVERT: B 635 LEU cc_start: 0.9700 (mm) cc_final: 0.9441 (mm) REVERT: B 710 MET cc_start: 0.9530 (mmt) cc_final: 0.9237 (mpp) outliers start: 25 outliers final: 20 residues processed: 103 average time/residue: 0.0611 time to fit residues: 10.5916 Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.075696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053838 restraints weight = 37530.845| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 5.09 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9496 Z= 0.159 Angle : 0.615 11.986 12874 Z= 0.313 Chirality : 0.040 0.245 1486 Planarity : 0.003 0.039 1632 Dihedral : 5.843 50.984 1338 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.32 % Allowed : 32.53 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.24), residues: 1170 helix: 2.24 (0.19), residues: 756 sheet: -0.14 (0.59), residues: 62 loop : -1.96 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.014 0.001 TYR B 465 PHE 0.023 0.001 PHE A 418 TRP 0.023 0.001 TRP A 822 HIS 0.002 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 9496) covalent geometry : angle 0.61466 / 0.31 (12874) hydrogen bonds : bond 0.06247 / 4.13 ( 613) hydrogen bonds : angle 4.11525 / 3.08 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8873 (tp30) REVERT: A 822 TRP cc_start: 0.8814 (p-90) cc_final: 0.8412 (p-90) REVERT: B 374 ASP cc_start: 0.9280 (m-30) cc_final: 0.9049 (t0) REVERT: B 455 ASP cc_start: 0.8642 (p0) cc_final: 0.8437 (p0) REVERT: B 635 LEU cc_start: 0.9674 (mm) cc_final: 0.9381 (mm) REVERT: B 710 MET cc_start: 0.9552 (mmt) cc_final: 0.9336 (mpp) outliers start: 23 outliers final: 22 residues processed: 106 average time/residue: 0.0552 time to fit residues: 9.6802 Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.076928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054741 restraints weight = 38090.972| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 5.20 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9496 Z= 0.134 Angle : 0.611 11.810 12874 Z= 0.306 Chirality : 0.040 0.242 1486 Planarity : 0.003 0.041 1632 Dihedral : 5.809 52.646 1338 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.32 % Allowed : 32.42 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1170 helix: 2.28 (0.19), residues: 756 sheet: -0.25 (0.58), residues: 62 loop : -1.91 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.010 0.001 TYR B 536 PHE 0.014 0.001 PHE A 325 TRP 0.023 0.002 TRP A 822 HIS 0.002 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 9496) covalent geometry : angle 0.61139 / 0.31 (12874) hydrogen bonds : bond 0.05825 / 3.85 ( 613) hydrogen bonds : angle 4.00028 / 3.01 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.8916 (pp30) REVERT: A 355 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8838 (tp30) REVERT: A 442 MET cc_start: 0.9272 (tmm) cc_final: 0.9003 (tmm) REVERT: A 822 TRP cc_start: 0.8864 (p-90) cc_final: 0.8465 (p-90) REVERT: B 338 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8937 (pp30) REVERT: B 374 ASP cc_start: 0.9287 (m-30) cc_final: 0.9052 (t0) REVERT: B 455 ASP cc_start: 0.8678 (p0) cc_final: 0.8446 (p0) REVERT: B 562 GLU cc_start: 0.9586 (mm-30) cc_final: 0.9354 (mm-30) REVERT: B 635 LEU cc_start: 0.9659 (mm) cc_final: 0.9363 (mm) REVERT: B 710 MET cc_start: 0.9567 (mmt) cc_final: 0.9328 (mpp) outliers start: 23 outliers final: 19 residues processed: 103 average time/residue: 0.0652 time to fit residues: 11.0129 Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 0.0170 chunk 94 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 21 optimal weight: 0.0570 chunk 55 optimal weight: 30.0000 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.076140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054393 restraints weight = 37448.823| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 5.06 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9496 Z= 0.142 Angle : 0.611 11.467 12874 Z= 0.307 Chirality : 0.040 0.244 1486 Planarity : 0.003 0.039 1632 Dihedral : 5.778 53.846 1338 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.63 % Allowed : 32.32 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1170 helix: 2.23 (0.19), residues: 760 sheet: -0.31 (0.58), residues: 62 loop : -1.89 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.012 0.001 TYR B 465 PHE 0.021 0.001 PHE A 418 TRP 0.022 0.001 TRP A 822 HIS 0.002 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9496) covalent geometry : angle 0.61119 / 0.31 (12874) hydrogen bonds : bond 0.05839 / 3.86 ( 613) hydrogen bonds : angle 4.02458 / 3.03 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.19 seconds wall clock time: 29 minutes 24.93 seconds (1764.93 seconds total)