Starting phenix.real_space_refine on Wed Jun 26 05:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr3_39534/06_2024/8yr3_39534_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr3_39534/06_2024/8yr3_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr3_39534/06_2024/8yr3_39534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr3_39534/06_2024/8yr3_39534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr3_39534/06_2024/8yr3_39534_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr3_39534/06_2024/8yr3_39534_updated.pdb" } resolution = 3.2 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= 0.016 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 Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 678": "OD1" <-> "OD2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 799": "OD1" <-> "OD2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B ASP 576": "OD1" <-> "OD2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 678": "OD1" <-> "OD2" Residue "B ASP 799": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/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: 5.62, per 1000 atoms: 0.60 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 - 3.50 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: 3.83 Conformation dependent library (CDL) restraints added in 1.8 seconds 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... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 65.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 262 through 294 Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 325 through 354 removed outlier: 4.583A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 366 through 390 removed outlier: 3.653A pdb=" N LEU A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 Processing helix chain 'A' and resid 413 through 456 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) removed outlier: 3.947A pdb=" N SER A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 469 through 521 Processing helix chain 'A' and resid 528 through 569 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 628 through 637 removed outlier: 3.668A pdb=" N PHE A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 680 through 687 removed outlier: 4.814A pdb=" N GLY A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 703 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 759 through 773 Processing helix chain 'A' and resid 785 through 789 removed outlier: 4.063A pdb=" N VAL A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 262 through 294 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 299 through 315 Processing helix chain 'B' and resid 325 through 354 removed outlier: 4.588A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 366 through 390 removed outlier: 3.785A pdb=" N LEU B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 412 through 456 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) removed outlier: 3.979A pdb=" N SER B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 469 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 527 through 569 removed outlier: 4.101A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Proline residue: B 543 - end of helix removed outlier: 5.413A pdb=" N TRP B 546 " --> pdb=" O MET B 542 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N PHE B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 654 through 656 No H-bonds generated for 'chain 'B' and resid 654 through 656' Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 680 through 687 removed outlier: 4.560A pdb=" N GLY B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 759 through 773 Processing helix chain 'B' and resid 785 through 789 removed outlier: 4.049A pdb=" N VAL B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 814 Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.503A pdb=" N GLN B 823 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.547A pdb=" N GLU A 591 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 648 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 593 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 646 " --> pdb=" O GLU A 593 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 778 through 781 Processing sheet with id= C, first strand: chain 'B' and resid 590 through 593 removed outlier: 3.833A pdb=" N ARG B 648 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 593 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS B 646 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 794 through 797 removed outlier: 8.272A pdb=" N LEU B 795 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 778 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU B 621 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 780 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLY B 623 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 781 " --> pdb=" O LEU B 750 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1641 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: 2.33 Time building geometry restraints manager: 4.09 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: 98.74 - 105.79: 125 105.79 - 112.85: 5088 112.85 - 119.90: 3334 119.90 - 126.95: 4226 126.95 - 134.01: 101 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: 4708 17.30 - 34.60: 667 34.60 - 51.90: 195 51.90 - 69.20: 32 69.20 - 86.50: 14 Dihedral angle restraints: 5616 sinusoidal: 2242 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 5613 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: 2013 2.77 - 3.30: 9287 3.30 - 3.83: 15264 3.83 - 4.37: 15943 4.37 - 4.90: 27628 Nonbonded interactions: 70135 Sorted by model distance: nonbonded pdb=" O THR A 428 " pdb=" OG1 THR A 432 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP A 678 " pdb=" N THR A 679 " model vdw 2.240 2.520 nonbonded pdb=" O THR B 320 " pdb=" OG1 THR B 320 " model vdw 2.247 2.440 nonbonded pdb=" ND2 ASN A 279 " pdb=" OD2 ASP A 397 " model vdw 2.255 2.520 nonbonded pdb=" NZ LYS B 245 " pdb=" OE1 GLU B 562 " model vdw 2.258 2.520 ... (remaining 70130 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' and (resid 240 through 826 or resid 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: 1.150 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: 4.690 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.890 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 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= 0.509 Angle : 1.029 20.736 12874 Z= 0.653 Chirality : 0.051 0.307 1486 Planarity : 0.011 0.247 1632 Dihedral : 17.688 86.505 3456 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (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 TRP 0.042 0.003 TRP A 822 HIS 0.004 0.001 HIS A 596 PHE 0.021 0.002 PHE A 585 TYR 0.020 0.002 TYR A 550 ARG 0.007 0.001 ARG B 552 *********************** 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 fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.064 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 416 ILE cc_start: 0.9143 (mm) cc_final: 0.8922 (mm) REVERT: B 455 ASP cc_start: 0.9282 (m-30) cc_final: 0.8736 (p0) REVERT: B 566 ASP cc_start: 0.9511 (t0) cc_final: 0.9192 (t0) 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: 0.2048 time to fit residues: 45.2585 Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 97 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 chunk 46 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 30.0000 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 502 ASN A 719 GLN A 733 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9496 Z= 0.205 Angle : 0.596 10.963 12874 Z= 0.308 Chirality : 0.041 0.237 1486 Planarity : 0.004 0.037 1632 Dihedral : 6.171 53.625 1348 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.94 % Allowed : 28.89 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1170 helix: 1.89 (0.19), residues: 738 sheet: 1.04 (0.67), residues: 62 loop : -2.28 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 434 HIS 0.006 0.001 HIS A 808 PHE 0.013 0.001 PHE A 325 TYR 0.018 0.001 TYR A 550 ARG 0.006 0.000 ARG B 365 *********************** 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 142 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 1.040 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 541 TYR cc_start: 0.9344 (t80) cc_final: 0.9065 (t80) REVERT: A 564 MET cc_start: 0.9592 (tmm) cc_final: 0.9346 (tmm) REVERT: A 566 ASP cc_start: 0.9601 (t0) cc_final: 0.9378 (t0) REVERT: A 614 MET cc_start: 0.9246 (tpp) cc_final: 0.8940 (tpt) REVERT: B 374 ASP cc_start: 0.9238 (m-30) cc_final: 0.9017 (t0) REVERT: B 416 ILE cc_start: 0.9109 (mm) cc_final: 0.8892 (mm) REVERT: B 454 VAL cc_start: 0.9532 (OUTLIER) cc_final: 0.9297 (p) REVERT: B 455 ASP cc_start: 0.9121 (m-30) cc_final: 0.8553 (p0) REVERT: B 474 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 566 ASP cc_start: 0.9517 (t0) cc_final: 0.9200 (t0) REVERT: B 668 VAL cc_start: 0.9583 (t) cc_final: 0.9320 (m) REVERT: B 749 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9290 (mm) outliers start: 39 outliers final: 20 residues processed: 137 average time/residue: 0.1627 time to fit residues: 33.6441 Evaluate side-chains 113 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 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: 9.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9496 Z= 0.186 Angle : 0.562 11.873 12874 Z= 0.289 Chirality : 0.039 0.181 1486 Planarity : 0.003 0.047 1632 Dihedral : 5.514 53.500 1339 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.64 % Allowed : 29.60 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1170 helix: 2.16 (0.19), residues: 746 sheet: 0.96 (0.66), residues: 62 loop : -2.25 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 822 HIS 0.003 0.001 HIS B 361 PHE 0.011 0.001 PHE A 325 TYR 0.015 0.001 TYR B 686 ARG 0.003 0.000 ARG A 435 *********************** 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 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 MET cc_start: 0.9587 (tmm) cc_final: 0.9310 (tmm) REVERT: A 566 ASP cc_start: 0.9595 (t0) cc_final: 0.9357 (t0) REVERT: A 614 MET cc_start: 0.9327 (tpp) cc_final: 0.9043 (tpt) REVERT: B 374 ASP cc_start: 0.9263 (m-30) cc_final: 0.9027 (t0) REVERT: B 455 ASP cc_start: 0.9130 (m-30) cc_final: 0.8562 (p0) REVERT: B 566 ASP cc_start: 0.9518 (t0) cc_final: 0.9194 (t0) REVERT: B 668 VAL cc_start: 0.9596 (t) cc_final: 0.9385 (m) REVERT: B 749 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9303 (mm) outliers start: 36 outliers final: 20 residues processed: 130 average time/residue: 0.1567 time to fit residues: 31.6316 Evaluate side-chains 113 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 406 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 672 ASP 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 406 SER Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN B 502 ASN B 677 ASN B 808 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9496 Z= 0.288 Angle : 0.607 10.408 12874 Z= 0.317 Chirality : 0.040 0.200 1486 Planarity : 0.003 0.046 1632 Dihedral : 5.211 55.138 1336 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.55 % Allowed : 29.80 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1170 helix: 2.18 (0.18), residues: 764 sheet: 0.75 (0.65), residues: 58 loop : -2.21 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 822 HIS 0.005 0.001 HIS A 361 PHE 0.014 0.001 PHE A 325 TYR 0.017 0.001 TYR B 465 ARG 0.004 0.000 ARG A 359 *********************** 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 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 91 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.9604 (t0) cc_final: 0.9355 (t0) REVERT: A 614 MET cc_start: 0.9410 (tpp) cc_final: 0.9134 (tpt) REVERT: A 822 TRP cc_start: 0.8644 (p-90) cc_final: 0.8427 (m-90) REVERT: A 824 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 455 ASP cc_start: 0.9185 (m-30) cc_final: 0.8729 (p0) REVERT: B 474 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 566 ASP cc_start: 0.9554 (t0) cc_final: 0.9225 (t0) REVERT: B 657 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.9035 (t) REVERT: B 749 LEU cc_start: 0.9547 (mm) cc_final: 0.9344 (mm) outliers start: 45 outliers final: 30 residues processed: 131 average time/residue: 0.1385 time to fit residues: 28.5858 Evaluate side-chains 118 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 406 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 618 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 672 ASP 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 A residue 824 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 740 THR 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 93 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN B 652 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9496 Z= 0.418 Angle : 0.695 9.791 12874 Z= 0.369 Chirality : 0.043 0.221 1486 Planarity : 0.004 0.049 1632 Dihedral : 5.397 50.765 1336 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.56 % Allowed : 29.90 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1170 helix: 1.81 (0.18), residues: 766 sheet: 0.19 (0.64), residues: 58 loop : -2.28 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 434 HIS 0.006 0.002 HIS A 361 PHE 0.023 0.002 PHE A 418 TYR 0.022 0.002 TYR B 465 ARG 0.009 0.001 ARG A 584 *********************** 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 139 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 84 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 MET cc_start: 0.9461 (tpp) cc_final: 0.9238 (tpt) REVERT: A 822 TRP cc_start: 0.8798 (p-90) cc_final: 0.8390 (p-90) REVERT: B 455 ASP cc_start: 0.9400 (m-30) cc_final: 0.9083 (p0) REVERT: B 566 ASP cc_start: 0.9601 (t0) cc_final: 0.9311 (t0) REVERT: B 676 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5947 (p90) REVERT: B 710 MET cc_start: 0.9514 (mmt) cc_final: 0.9219 (mpp) REVERT: B 749 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9270 (mm) outliers start: 55 outliers final: 39 residues processed: 132 average time/residue: 0.1564 time to fit residues: 31.6218 Evaluate side-chains 112 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 71 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 686 TYR 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 244 ARG 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 406 SER Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 682 ASP Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 733 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9496 Z= 0.177 Angle : 0.584 10.494 12874 Z= 0.299 Chirality : 0.040 0.221 1486 Planarity : 0.003 0.044 1632 Dihedral : 5.119 48.462 1336 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.03 % Allowed : 32.12 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1170 helix: 2.28 (0.19), residues: 760 sheet: 0.25 (0.65), residues: 58 loop : -2.15 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 434 HIS 0.002 0.001 HIS B 352 PHE 0.015 0.001 PHE A 418 TYR 0.012 0.001 TYR B 465 ARG 0.003 0.000 ARG A 584 *********************** 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 119 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.9081 (pt0) cc_final: 0.8877 (pt0) REVERT: A 614 MET cc_start: 0.9449 (tpp) cc_final: 0.9136 (tmm) REVERT: A 822 TRP cc_start: 0.8823 (p-90) cc_final: 0.8449 (p-90) REVERT: B 455 ASP cc_start: 0.9268 (m-30) cc_final: 0.8926 (p0) REVERT: B 566 ASP cc_start: 0.9569 (t0) cc_final: 0.9246 (t0) REVERT: B 749 LEU cc_start: 0.9515 (mm) cc_final: 0.9120 (mm) outliers start: 30 outliers final: 21 residues processed: 115 average time/residue: 0.1502 time to fit residues: 27.2054 Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 676 PHE 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 266 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 740 THR 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 12 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 44 optimal weight: 0.0370 chunk 66 optimal weight: 4.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 793 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9496 Z= 0.186 Angle : 0.597 12.328 12874 Z= 0.299 Chirality : 0.040 0.243 1486 Planarity : 0.003 0.042 1632 Dihedral : 4.880 46.813 1334 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.13 % Allowed : 32.42 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1170 helix: 2.31 (0.19), residues: 762 sheet: 0.36 (0.66), residues: 58 loop : -2.05 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 822 HIS 0.003 0.001 HIS A 361 PHE 0.016 0.001 PHE B 418 TYR 0.014 0.001 TYR B 465 ARG 0.003 0.000 ARG B 584 *********************** 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 113 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 82 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9342 (tmm) cc_final: 0.9058 (tmm) REVERT: A 614 MET cc_start: 0.9454 (tpp) cc_final: 0.9141 (tmm) REVERT: A 822 TRP cc_start: 0.8852 (p-90) cc_final: 0.8471 (p-90) REVERT: A 824 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (tp) REVERT: B 407 MET cc_start: 0.8805 (mmm) cc_final: 0.8588 (mmp) REVERT: B 455 ASP cc_start: 0.9200 (m-30) cc_final: 0.8924 (p0) REVERT: B 566 ASP cc_start: 0.9568 (t0) cc_final: 0.9246 (t0) REVERT: B 749 LEU cc_start: 0.9488 (mm) cc_final: 0.9203 (mm) outliers start: 31 outliers final: 24 residues processed: 110 average time/residue: 0.1526 time to fit residues: 26.3571 Evaluate side-chains 99 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 720 VAL 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 A residue 824 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 740 THR 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 33 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9496 Z= 0.200 Angle : 0.596 12.720 12874 Z= 0.301 Chirality : 0.040 0.251 1486 Planarity : 0.003 0.039 1632 Dihedral : 4.814 44.693 1334 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.23 % Allowed : 32.22 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1170 helix: 2.28 (0.19), residues: 764 sheet: 0.37 (0.66), residues: 58 loop : -2.05 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 822 HIS 0.003 0.001 HIS A 361 PHE 0.021 0.001 PHE A 418 TYR 0.014 0.001 TYR B 465 ARG 0.003 0.000 ARG B 589 *********************** 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 112 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9336 (tmm) cc_final: 0.9058 (tmm) REVERT: A 614 MET cc_start: 0.9450 (tpp) cc_final: 0.9151 (tmm) REVERT: A 822 TRP cc_start: 0.8873 (p-90) cc_final: 0.8494 (p-90) REVERT: A 824 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8784 (tt) REVERT: B 566 ASP cc_start: 0.9563 (t0) cc_final: 0.9242 (t0) REVERT: B 710 MET cc_start: 0.9516 (mmt) cc_final: 0.9240 (mpp) REVERT: B 749 LEU cc_start: 0.9490 (mm) cc_final: 0.9199 (mm) outliers start: 32 outliers final: 28 residues processed: 110 average time/residue: 0.1426 time to fit residues: 25.3497 Evaluate side-chains 103 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 293 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 461 GLU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 720 VAL 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 A residue 794 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 740 THR 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 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9496 Z= 0.164 Angle : 0.600 11.722 12874 Z= 0.297 Chirality : 0.040 0.258 1486 Planarity : 0.003 0.039 1632 Dihedral : 4.749 42.591 1334 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.73 % Allowed : 33.43 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1170 helix: 2.34 (0.19), residues: 748 sheet: 0.53 (0.67), residues: 58 loop : -1.88 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 822 HIS 0.002 0.001 HIS A 361 PHE 0.015 0.001 PHE B 418 TYR 0.011 0.001 TYR B 465 ARG 0.002 0.000 ARG B 584 *********************** 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 111 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9335 (tmm) cc_final: 0.9072 (tmm) REVERT: A 566 ASP cc_start: 0.9585 (t0) cc_final: 0.9309 (t0) REVERT: A 614 MET cc_start: 0.9438 (tpp) cc_final: 0.9133 (tmm) REVERT: A 822 TRP cc_start: 0.8855 (p-90) cc_final: 0.8480 (p-90) REVERT: A 824 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8770 (tt) REVERT: B 566 ASP cc_start: 0.9551 (t0) cc_final: 0.9229 (t0) REVERT: B 710 MET cc_start: 0.9511 (mmt) cc_final: 0.9246 (mpp) REVERT: B 749 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9236 (mm) outliers start: 27 outliers final: 19 residues processed: 108 average time/residue: 0.1422 time to fit residues: 24.6548 Evaluate side-chains 98 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 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 52 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 316 GLN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9496 Z= 0.250 Angle : 0.629 11.124 12874 Z= 0.317 Chirality : 0.040 0.246 1486 Planarity : 0.003 0.038 1632 Dihedral : 4.758 41.651 1334 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.63 % Allowed : 33.74 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1170 helix: 2.26 (0.19), residues: 768 sheet: 0.40 (0.66), residues: 58 loop : -1.99 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 822 HIS 0.004 0.001 HIS A 361 PHE 0.020 0.001 PHE A 418 TYR 0.014 0.001 TYR B 465 ARG 0.003 0.000 ARG B 584 ********************** 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 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: A 442 MET cc_start: 0.9335 (tmm) cc_final: 0.9042 (tmm) REVERT: A 566 ASP cc_start: 0.9596 (t0) cc_final: 0.9317 (t0) REVERT: A 614 MET cc_start: 0.9459 (tpp) cc_final: 0.9152 (tmm) REVERT: A 822 TRP cc_start: 0.8884 (p-90) cc_final: 0.8492 (p-90) REVERT: A 824 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 455 ASP cc_start: 0.8883 (p0) cc_final: 0.8577 (p0) REVERT: B 566 ASP cc_start: 0.9568 (t0) cc_final: 0.9247 (t0) REVERT: B 710 MET cc_start: 0.9530 (mmt) cc_final: 0.9324 (mpp) REVERT: B 749 LEU cc_start: 0.9505 (mm) cc_final: 0.9236 (mm) outliers start: 26 outliers final: 23 residues processed: 101 average time/residue: 0.1512 time to fit residues: 24.5795 Evaluate side-chains 100 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 75 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 461 GLU 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 720 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 740 THR 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 84 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.074725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052688 restraints weight = 37622.801| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.89 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9496 Z= 0.242 Angle : 0.629 10.927 12874 Z= 0.318 Chirality : 0.041 0.252 1486 Planarity : 0.003 0.038 1632 Dihedral : 4.803 40.113 1334 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.73 % Allowed : 33.64 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1170 helix: 2.25 (0.19), residues: 770 sheet: 0.41 (0.67), residues: 58 loop : -1.98 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 434 HIS 0.003 0.001 HIS A 361 PHE 0.015 0.001 PHE A 325 TYR 0.019 0.001 TYR B 599 ARG 0.003 0.000 ARG B 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.12 seconds wall clock time: 34 minutes 4.17 seconds (2044.17 seconds total)