Starting phenix.real_space_refine on Fri Feb 16 12:39:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5b_31464/02_2024/7f5b_31464_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5b_31464/02_2024/7f5b_31464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5b_31464/02_2024/7f5b_31464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5b_31464/02_2024/7f5b_31464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5b_31464/02_2024/7f5b_31464_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5b_31464/02_2024/7f5b_31464_updated.pdb" } resolution = 3.9 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= 0.003 sd= 0.091 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 Ca 1 9.91 5 S 97 5.16 5 C 9876 2.51 5 N 2489 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 503": "NH1" <-> "NH2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B GLU 743": "OE1" <-> "OE2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C GLU 841": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D GLU 743": "OE1" <-> "OE2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15328 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3454 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 419} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3416 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 415} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3458 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain: "D" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3315 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 402} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1506 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGT:plan-1': 1, 'PGT:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 8.22, per 1000 atoms: 0.54 Number of scatterers: 15328 At special positions: 0 Unit cell: (121.04, 116.96, 149.6, 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) Ca 1 19.99 S 97 16.00 O 2865 8.00 N 2489 7.00 C 9876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=2.01 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.02 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.04 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1001 " - " ASN A 751 " " NAG A1002 " - " ASN A 546 " " NAG B1102 " - " ASN B 751 " " NAG C1001 " - " ASN C 546 " " NAG C1002 " - " ASN C 751 " " NAG D1001 " - " ASN D 751 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN D 546 " Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 2.5 seconds 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 9 sheets defined 41.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 462 through 474 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 561 through 583 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 631 through 664 removed outlier: 3.878A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'A' and resid 722 through 730 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 825 through 850 removed outlier: 3.599A pdb=" N ASN A 849 " --> pdb=" O LYS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 462 through 474 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.123A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 removed outlier: 4.181A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 556' Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.578A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 619 Processing helix chain 'B' and resid 632 through 661 removed outlier: 4.032A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 674 No H-bonds generated for 'chain 'B' and resid 671 through 674' Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.944A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 798 Processing helix chain 'B' and resid 817 through 849 removed outlier: 6.932A pdb=" N GLY B 822 " --> pdb=" O GLN B 818 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE B 823 " --> pdb=" O ASN B 819 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 824 " --> pdb=" O ILE B 820 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 862 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 462 through 474 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 563 through 582 Processing helix chain 'C' and resid 608 through 620 Processing helix chain 'C' and resid 631 through 662 Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 700 through 712 Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 739 through 748 removed outlier: 3.667A pdb=" N ARG C 748 " --> pdb=" O PHE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 787 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 824 through 847 removed outlier: 3.602A pdb=" N LYS C 845 " --> pdb=" O PHE C 842 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 847 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 866 Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 462 through 474 removed outlier: 3.682A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 521 through 525 removed outlier: 3.713A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 521 through 525' Processing helix chain 'D' and resid 561 through 583 removed outlier: 3.766A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 619 Processing helix chain 'D' and resid 634 through 660 removed outlier: 3.884A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 674 No H-bonds generated for 'chain 'D' and resid 671 through 674' Processing helix chain 'D' and resid 690 through 694 Processing helix chain 'D' and resid 703 through 711 Processing helix chain 'D' and resid 721 through 730 Processing helix chain 'D' and resid 739 through 748 removed outlier: 4.399A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 4.175A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 799 removed outlier: 3.796A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 849 Processing helix chain 'E' and resid 340 through 343 No H-bonds generated for 'chain 'E' and resid 340 through 343' Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.826A pdb=" N VAL E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 437 Processing sheet with id= B, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.143A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 536 " --> pdb=" O LYS B 762 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.996A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 433 through 437 Processing sheet with id= E, first strand: chain 'C' and resid 444 through 446 Processing sheet with id= F, first strand: chain 'C' and resid 540 through 543 removed outlier: 4.125A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 755 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 538 through 541 Processing sheet with id= H, first strand: chain 'E' and resid 206 through 212 removed outlier: 3.758A pdb=" N CYS E 207 " --> pdb=" O MET E 274 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET E 274 " --> pdb=" O CYS E 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 271 " --> pdb=" O TYR E 242 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL E 239 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP E 243 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU E 251 " --> pdb=" O ASP E 243 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 263 through 265 removed outlier: 6.953A pdb=" N ARG E 286 " --> pdb=" O LEU E 224 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1587 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: 3.81 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3646 1.33 - 1.45: 3238 1.45 - 1.57: 8623 1.57 - 1.69: 0 1.69 - 1.81: 157 Bond restraints: 15664 Sorted by residual: bond pdb=" N PRO E 325 " pdb=" CA PRO E 325 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.48e+01 bond pdb=" N THR E 301 " pdb=" CA THR E 301 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" CA ALA E 323 " pdb=" CB ALA E 323 " ideal model delta sigma weight residual 1.528 1.486 0.043 1.56e-02 4.11e+03 7.54e+00 bond pdb=" N CYS E 297 " pdb=" CA CYS E 297 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.27e-02 6.20e+03 6.56e+00 bond pdb=" N PHE E 302 " pdb=" CA PHE E 302 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.54e+00 ... (remaining 15659 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.07: 269 105.07 - 112.35: 7890 112.35 - 119.64: 5223 119.64 - 126.93: 7624 126.93 - 134.21: 192 Bond angle restraints: 21198 Sorted by residual: angle pdb=" N VAL E 293 " pdb=" CA VAL E 293 " pdb=" C VAL E 293 " ideal model delta sigma weight residual 111.58 104.64 6.94 1.06e+00 8.90e-01 4.28e+01 angle pdb=" N ASN D 751 " pdb=" CA ASN D 751 " pdb=" C ASN D 751 " ideal model delta sigma weight residual 114.16 105.77 8.39 1.48e+00 4.57e-01 3.21e+01 angle pdb=" C LEU C 556 " pdb=" N ASN C 557 " pdb=" CA ASN C 557 " ideal model delta sigma weight residual 119.78 125.72 -5.94 1.24e+00 6.50e-01 2.30e+01 angle pdb=" CA PRO E 325 " pdb=" C PRO E 325 " pdb=" O PRO E 325 " ideal model delta sigma weight residual 121.34 115.91 5.43 1.14e+00 7.69e-01 2.27e+01 angle pdb=" C PRO E 325 " pdb=" CA PRO E 325 " pdb=" CB PRO E 325 " ideal model delta sigma weight residual 111.46 105.61 5.85 1.29e+00 6.01e-01 2.06e+01 ... (remaining 21193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 8700 21.82 - 43.63: 651 43.63 - 65.45: 68 65.45 - 87.26: 39 87.26 - 109.08: 29 Dihedral angle restraints: 9487 sinusoidal: 3944 harmonic: 5543 Sorted by residual: dihedral pdb=" CB CYS E 316 " pdb=" SG CYS E 316 " pdb=" SG CYS E 331 " pdb=" CB CYS E 331 " ideal model delta sinusoidal sigma weight residual -86.00 -158.69 72.69 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CA ASN E 311 " pdb=" C ASN E 311 " pdb=" N ASN E 312 " pdb=" CA ASN E 312 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ARG E 284 " pdb=" C ARG E 284 " pdb=" N PHE E 285 " pdb=" CA PHE E 285 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 9484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2268 0.093 - 0.186: 119 0.186 - 0.279: 10 0.279 - 0.372: 1 0.372 - 0.465: 2 Chirality restraints: 2400 Sorted by residual: chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA TYR E 324 " pdb=" N TYR E 324 " pdb=" C TYR E 324 " pdb=" CB TYR E 324 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 2397 not shown) Planarity restraints: 2667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 292 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C PHE E 292 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE E 292 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 293 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 451 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO B 452 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 613 " 0.019 2.00e-02 2.50e+03 1.36e-02 4.65e+00 pdb=" CG TRP C 613 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 613 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 613 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 613 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 613 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 613 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 613 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 613 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 613 " 0.005 2.00e-02 2.50e+03 ... (remaining 2664 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 334 2.67 - 3.23: 15792 3.23 - 3.78: 23294 3.78 - 4.34: 30313 4.34 - 4.90: 47827 Nonbonded interactions: 117560 Sorted by model distance: nonbonded pdb=" O GLY D 489 " pdb=" NH1 ARG D 523 " model vdw 2.110 2.520 nonbonded pdb=" O LEU B 674 " pdb=" OH TYR B 682 " model vdw 2.117 2.440 nonbonded pdb=" O LEU A 674 " pdb=" OH TYR A 682 " model vdw 2.153 2.440 nonbonded pdb=" O ASN C 596 " pdb=" OD1 ASN C 596 " model vdw 2.211 3.040 nonbonded pdb=" O TRP A 798 " pdb=" ND2 ASN A 802 " model vdw 2.213 2.520 ... (remaining 117555 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 431 through 527 or (resid 528 and (name N or name CA or na \ me C or name O or name CB )) or resid 529 through 663 or (resid 664 and (name N \ or name CA or name C or name O or name CB )) or resid 665 through 850)) selection = (chain 'B' and (resid 431 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 691 or (resid 692 and (name N \ or name CA or name C or name O or name CB )) or resid 693 through 850)) selection = (chain 'C' and (resid 431 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 663 or (resid \ 664 and (name N or name CA or name C or name O or name CB )) or resid 665 throug \ h 691 or (resid 692 and (name N or name CA or name C or name O or name CB )) or \ resid 693 through 850)) selection = (chain 'D' and (resid 431 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 691 or (resid \ 692 and (name N or name CA or name C or name O or name CB )) or resid 693 throug \ h 850)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.830 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.004 0.052 15664 Z= 0.275 Angle : 0.818 8.877 21198 Z= 0.458 Chirality : 0.050 0.465 2400 Planarity : 0.004 0.055 2659 Dihedral : 16.744 109.077 5916 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.75 % Favored : 91.20 % Rotamer: Outliers : 0.18 % Allowed : 0.30 % Favored : 99.52 % Cbeta Deviations : 0.06 % 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: -1.83 (0.19), residues: 1909 helix: 0.61 (0.18), residues: 827 sheet: -1.47 (0.53), residues: 100 loop : -2.99 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 613 HIS 0.007 0.001 HIS E 230 PHE 0.022 0.002 PHE C 642 TYR 0.028 0.002 TYR E 324 ARG 0.007 0.001 ARG D 775 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9040 (m) cc_final: 0.8784 (p) REVERT: A 610 ASN cc_start: 0.8241 (t0) cc_final: 0.8022 (t0) REVERT: A 633 THR cc_start: 0.8852 (p) cc_final: 0.8462 (m) REVERT: A 794 MET cc_start: 0.8210 (mpp) cc_final: 0.7929 (mpp) REVERT: A 867 MET cc_start: 0.4852 (pmm) cc_final: 0.3214 (mmm) REVERT: B 568 LEU cc_start: 0.8514 (mm) cc_final: 0.8263 (mt) REVERT: B 705 MET cc_start: 0.7416 (mtm) cc_final: 0.6544 (mpp) REVERT: C 691 MET cc_start: 0.8370 (ttp) cc_final: 0.8161 (ttp) REVERT: C 705 MET cc_start: 0.8836 (mmm) cc_final: 0.8204 (mmm) REVERT: D 478 TYR cc_start: 0.6613 (m-10) cc_final: 0.6350 (m-10) REVERT: D 588 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 632 SER cc_start: 0.9030 (m) cc_final: 0.8721 (m) REVERT: E 243 ASP cc_start: 0.7071 (p0) cc_final: 0.6693 (p0) REVERT: E 324 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6987 (m-80) outliers start: 3 outliers final: 0 residues processed: 247 average time/residue: 0.2242 time to fit residues: 87.6689 Evaluate side-chains 193 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.0000 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 596 ASN D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15664 Z= 0.339 Angle : 0.734 7.756 21198 Z= 0.374 Chirality : 0.047 0.431 2400 Planarity : 0.004 0.058 2659 Dihedral : 11.904 89.134 2326 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.81 % Allowed : 10.08 % Favored : 88.10 % 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: -1.86 (0.19), residues: 1909 helix: 0.57 (0.18), residues: 828 sheet: -1.56 (0.50), residues: 117 loop : -3.00 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 613 HIS 0.004 0.001 HIS B 792 PHE 0.030 0.002 PHE A 533 TYR 0.019 0.002 TYR C 682 ARG 0.005 0.000 ARG D 748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8242 (mmm) cc_final: 0.8008 (mmt) REVERT: A 575 SER cc_start: 0.9035 (m) cc_final: 0.8783 (p) REVERT: A 610 ASN cc_start: 0.8257 (t0) cc_final: 0.7988 (t0) REVERT: A 709 MET cc_start: 0.8117 (mpp) cc_final: 0.7701 (mpp) REVERT: A 867 MET cc_start: 0.4963 (pmm) cc_final: 0.3402 (mmm) REVERT: B 620 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8584 (mmt) REVERT: D 583 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.8063 (mmm160) REVERT: D 588 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7847 (mm-30) REVERT: D 632 SER cc_start: 0.9023 (m) cc_final: 0.8744 (m) REVERT: E 324 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6750 (m-80) outliers start: 30 outliers final: 16 residues processed: 222 average time/residue: 0.2236 time to fit residues: 79.0210 Evaluate side-chains 207 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 353 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 172 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 58 optimal weight: 0.0020 chunk 138 optimal weight: 1.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15664 Z= 0.195 Angle : 0.654 8.560 21198 Z= 0.327 Chirality : 0.045 0.449 2400 Planarity : 0.004 0.056 2659 Dihedral : 9.634 73.904 2326 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.51 % Allowed : 14.43 % Favored : 84.06 % 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: -1.60 (0.20), residues: 1909 helix: 0.82 (0.19), residues: 827 sheet: -1.47 (0.50), residues: 115 loop : -2.87 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 613 HIS 0.003 0.001 HIS B 792 PHE 0.025 0.002 PHE D 555 TYR 0.022 0.001 TYR C 682 ARG 0.004 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9118 (m) cc_final: 0.8825 (p) REVERT: A 610 ASN cc_start: 0.8167 (t0) cc_final: 0.7931 (t0) REVERT: A 705 MET cc_start: 0.8994 (mtm) cc_final: 0.8304 (ptp) REVERT: A 709 MET cc_start: 0.8046 (mpp) cc_final: 0.7726 (mpp) REVERT: A 867 MET cc_start: 0.4958 (pmm) cc_final: 0.3428 (mmm) REVERT: B 529 PHE cc_start: 0.8540 (m-10) cc_final: 0.8322 (m-80) REVERT: B 620 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8306 (mmm) REVERT: C 620 MET cc_start: 0.8694 (mmt) cc_final: 0.8377 (mmt) REVERT: D 583 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8104 (mmm160) REVERT: D 584 PHE cc_start: 0.7227 (m-10) cc_final: 0.6479 (t80) REVERT: D 588 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7830 (mm-30) REVERT: D 632 SER cc_start: 0.8924 (m) cc_final: 0.8624 (m) REVERT: D 691 MET cc_start: 0.8389 (mtp) cc_final: 0.8151 (mtp) REVERT: E 309 CYS cc_start: 0.5206 (m) cc_final: 0.1809 (m) REVERT: E 324 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: E 326 TRP cc_start: 0.8181 (m100) cc_final: 0.7930 (m100) outliers start: 25 outliers final: 13 residues processed: 223 average time/residue: 0.2253 time to fit residues: 79.4534 Evaluate side-chains 204 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 173 optimal weight: 0.0010 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 ASN D 819 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15664 Z= 0.357 Angle : 0.710 8.097 21198 Z= 0.359 Chirality : 0.047 0.455 2400 Planarity : 0.004 0.054 2659 Dihedral : 8.631 62.595 2326 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.54 % Allowed : 16.36 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.70 (0.20), residues: 1909 helix: 0.73 (0.19), residues: 829 sheet: -1.50 (0.50), residues: 119 loop : -2.93 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 706 HIS 0.003 0.001 HIS C 508 PHE 0.033 0.002 PHE A 533 TYR 0.023 0.001 TYR C 682 ARG 0.003 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9183 (m) cc_final: 0.8839 (p) REVERT: A 610 ASN cc_start: 0.8228 (t0) cc_final: 0.7983 (t0) REVERT: A 709 MET cc_start: 0.8058 (mpp) cc_final: 0.7684 (mpp) REVERT: A 718 VAL cc_start: 0.7941 (t) cc_final: 0.7730 (t) REVERT: B 529 PHE cc_start: 0.8588 (m-10) cc_final: 0.8307 (m-80) REVERT: B 620 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8497 (mmt) REVERT: D 579 PHE cc_start: 0.8016 (t80) cc_final: 0.7793 (t80) REVERT: D 583 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7998 (mmm-85) REVERT: D 588 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 632 SER cc_start: 0.8980 (m) cc_final: 0.8714 (m) REVERT: E 324 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6709 (m-80) outliers start: 42 outliers final: 22 residues processed: 226 average time/residue: 0.2320 time to fit residues: 82.0257 Evaluate side-chains 213 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15664 Z= 0.250 Angle : 0.658 9.479 21198 Z= 0.329 Chirality : 0.045 0.483 2400 Planarity : 0.004 0.058 2659 Dihedral : 7.762 59.846 2326 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.02 % Allowed : 17.63 % Favored : 79.35 % 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: -1.59 (0.20), residues: 1909 helix: 0.84 (0.19), residues: 827 sheet: -1.39 (0.50), residues: 118 loop : -2.89 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 613 HIS 0.002 0.000 HIS C 508 PHE 0.027 0.002 PHE D 555 TYR 0.023 0.001 TYR C 733 ARG 0.003 0.000 ARG D 748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7631 (mmt) cc_final: 0.7355 (mmt) REVERT: A 575 SER cc_start: 0.9145 (m) cc_final: 0.8793 (p) REVERT: A 610 ASN cc_start: 0.8179 (t0) cc_final: 0.7942 (t0) REVERT: A 620 MET cc_start: 0.8694 (ttm) cc_final: 0.8415 (ttm) REVERT: A 705 MET cc_start: 0.9143 (mtm) cc_final: 0.8172 (ptp) REVERT: A 709 MET cc_start: 0.8102 (mpp) cc_final: 0.7701 (mpp) REVERT: A 718 VAL cc_start: 0.7861 (t) cc_final: 0.7431 (t) REVERT: A 723 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.5816 (pt0) REVERT: A 867 MET cc_start: 0.4939 (pmm) cc_final: 0.3519 (mmm) REVERT: B 620 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8430 (mmt) REVERT: C 705 MET cc_start: 0.9395 (mmm) cc_final: 0.8191 (mmm) REVERT: D 588 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7866 (mm-30) REVERT: D 632 SER cc_start: 0.8939 (m) cc_final: 0.8673 (m) REVERT: E 324 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: E 326 TRP cc_start: 0.8144 (m100) cc_final: 0.7939 (m100) outliers start: 50 outliers final: 29 residues processed: 235 average time/residue: 0.2255 time to fit residues: 83.8429 Evaluate side-chains 223 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 15 optimal weight: 0.0050 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 792 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15664 Z= 0.179 Angle : 0.631 9.283 21198 Z= 0.316 Chirality : 0.044 0.504 2400 Planarity : 0.004 0.062 2659 Dihedral : 7.056 59.994 2326 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.72 % Allowed : 19.38 % Favored : 77.90 % 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: -1.39 (0.20), residues: 1909 helix: 0.98 (0.19), residues: 832 sheet: -1.34 (0.50), residues: 115 loop : -2.77 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 613 HIS 0.003 0.000 HIS E 305 PHE 0.024 0.001 PHE D 555 TYR 0.023 0.001 TYR C 733 ARG 0.004 0.000 ARG D 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9182 (m) cc_final: 0.8817 (p) REVERT: A 610 ASN cc_start: 0.8099 (t0) cc_final: 0.7893 (t0) REVERT: A 709 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7601 (mpp) REVERT: A 723 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5708 (pt0) REVERT: A 867 MET cc_start: 0.4915 (pmm) cc_final: 0.3447 (mmm) REVERT: B 603 GLU cc_start: 0.4059 (mm-30) cc_final: 0.3751 (mm-30) REVERT: D 588 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7889 (tm-30) REVERT: D 632 SER cc_start: 0.8873 (m) cc_final: 0.8615 (m) REVERT: D 705 MET cc_start: 0.9354 (mmm) cc_final: 0.9028 (tpt) REVERT: E 326 TRP cc_start: 0.8056 (m100) cc_final: 0.7837 (m100) outliers start: 45 outliers final: 25 residues processed: 235 average time/residue: 0.2265 time to fit residues: 83.8231 Evaluate side-chains 216 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 183 optimal weight: 0.0040 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15664 Z= 0.280 Angle : 0.669 8.919 21198 Z= 0.336 Chirality : 0.045 0.526 2400 Planarity : 0.004 0.058 2659 Dihedral : 6.816 59.521 2324 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.14 % Allowed : 19.81 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.20), residues: 1909 helix: 0.91 (0.19), residues: 831 sheet: -1.40 (0.48), residues: 120 loop : -2.78 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 613 HIS 0.005 0.001 HIS B 792 PHE 0.028 0.002 PHE A 533 TYR 0.021 0.001 TYR C 733 ARG 0.003 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9204 (m) cc_final: 0.8809 (p) REVERT: A 610 ASN cc_start: 0.8176 (t0) cc_final: 0.7951 (t0) REVERT: A 620 MET cc_start: 0.8754 (mmm) cc_final: 0.8285 (ttm) REVERT: A 709 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7581 (mpp) REVERT: A 723 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5867 (pt0) REVERT: A 867 MET cc_start: 0.5128 (pmm) cc_final: 0.3586 (mmm) REVERT: B 603 GLU cc_start: 0.4100 (mm-30) cc_final: 0.3848 (mm-30) REVERT: B 620 MET cc_start: 0.8392 (mmm) cc_final: 0.7649 (mmm) REVERT: C 590 TYR cc_start: 0.7271 (t80) cc_final: 0.7059 (t80) REVERT: D 588 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7889 (tm-30) REVERT: D 632 SER cc_start: 0.8891 (m) cc_final: 0.8629 (m) outliers start: 52 outliers final: 37 residues processed: 227 average time/residue: 0.2420 time to fit residues: 87.6668 Evaluate side-chains 227 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN D 819 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15664 Z= 0.175 Angle : 0.633 9.928 21198 Z= 0.316 Chirality : 0.044 0.520 2400 Planarity : 0.004 0.060 2659 Dihedral : 6.514 59.972 2324 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.78 % Allowed : 20.95 % Favored : 76.27 % 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: -1.32 (0.20), residues: 1909 helix: 1.02 (0.19), residues: 833 sheet: -1.14 (0.52), residues: 109 loop : -2.72 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 613 HIS 0.003 0.000 HIS B 792 PHE 0.025 0.001 PHE D 555 TYR 0.017 0.001 TYR C 682 ARG 0.005 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9178 (m) cc_final: 0.8765 (p) REVERT: A 620 MET cc_start: 0.8709 (mmm) cc_final: 0.8417 (ttm) REVERT: A 705 MET cc_start: 0.9010 (mtm) cc_final: 0.8271 (ptp) REVERT: A 709 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7579 (mpp) REVERT: A 723 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5666 (pt0) REVERT: A 867 MET cc_start: 0.5072 (pmm) cc_final: 0.3533 (mmm) REVERT: B 603 GLU cc_start: 0.3853 (mm-30) cc_final: 0.3637 (mm-30) REVERT: B 620 MET cc_start: 0.8387 (mmm) cc_final: 0.7778 (mmm) REVERT: C 441 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7543 (mt-10) REVERT: C 861 MET cc_start: 0.7369 (mpp) cc_final: 0.6807 (tmm) REVERT: D 588 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7812 (mm-30) REVERT: D 632 SER cc_start: 0.8839 (m) cc_final: 0.8548 (m) REVERT: D 705 MET cc_start: 0.9347 (mmm) cc_final: 0.9058 (tpt) outliers start: 46 outliers final: 29 residues processed: 240 average time/residue: 0.2275 time to fit residues: 85.5565 Evaluate side-chains 224 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.5980 chunk 170 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN B 792 HIS ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15664 Z= 0.231 Angle : 0.656 9.188 21198 Z= 0.329 Chirality : 0.045 0.540 2400 Planarity : 0.004 0.059 2659 Dihedral : 6.474 59.720 2324 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.84 % Allowed : 21.44 % Favored : 75.72 % 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: -1.34 (0.20), residues: 1909 helix: 0.98 (0.19), residues: 832 sheet: -1.19 (0.49), residues: 119 loop : -2.72 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 613 HIS 0.003 0.000 HIS E 330 PHE 0.025 0.001 PHE D 555 TYR 0.021 0.001 TYR C 682 ARG 0.002 0.000 ARG D 748 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9192 (m) cc_final: 0.8776 (p) REVERT: A 705 MET cc_start: 0.9057 (mtm) cc_final: 0.8269 (ptp) REVERT: A 709 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7534 (mpp) REVERT: A 723 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5746 (pt0) REVERT: A 867 MET cc_start: 0.5116 (pmm) cc_final: 0.3565 (mmm) REVERT: B 603 GLU cc_start: 0.3831 (mm-30) cc_final: 0.3611 (mm-30) REVERT: B 620 MET cc_start: 0.8302 (mmm) cc_final: 0.7821 (mmm) REVERT: C 441 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7562 (mt-10) REVERT: C 709 MET cc_start: 0.9069 (mmm) cc_final: 0.8865 (mmm) REVERT: C 861 MET cc_start: 0.7276 (mpp) cc_final: 0.6802 (tmm) REVERT: D 588 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 632 SER cc_start: 0.8805 (m) cc_final: 0.8540 (m) REVERT: D 705 MET cc_start: 0.9353 (mmm) cc_final: 0.9033 (tpt) outliers start: 47 outliers final: 37 residues processed: 230 average time/residue: 0.2159 time to fit residues: 78.3275 Evaluate side-chains 228 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 792 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15664 Z= 0.208 Angle : 0.658 9.506 21198 Z= 0.329 Chirality : 0.044 0.537 2400 Planarity : 0.004 0.060 2659 Dihedral : 6.377 59.827 2324 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.66 % Allowed : 21.68 % Favored : 75.66 % 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 (0.20), residues: 1909 helix: 0.97 (0.19), residues: 832 sheet: -1.06 (0.51), residues: 109 loop : -2.69 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 613 HIS 0.002 0.000 HIS C 508 PHE 0.025 0.001 PHE D 555 TYR 0.026 0.001 TYR C 682 ARG 0.002 0.000 ARG E 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9178 (m) cc_final: 0.8764 (p) REVERT: A 620 MET cc_start: 0.8589 (ttm) cc_final: 0.8219 (ttm) REVERT: A 705 MET cc_start: 0.9045 (mtm) cc_final: 0.8270 (ptp) REVERT: A 709 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7520 (mpp) REVERT: A 723 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5727 (pt0) REVERT: A 867 MET cc_start: 0.5110 (pmm) cc_final: 0.3565 (mmm) REVERT: B 833 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8615 (tt) REVERT: C 441 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7609 (mt-10) REVERT: C 861 MET cc_start: 0.7226 (mpp) cc_final: 0.6824 (tmm) REVERT: D 588 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7751 (mm-30) REVERT: D 632 SER cc_start: 0.8801 (m) cc_final: 0.8555 (m) REVERT: D 705 MET cc_start: 0.9338 (mmm) cc_final: 0.9031 (tpt) outliers start: 44 outliers final: 35 residues processed: 225 average time/residue: 0.2285 time to fit residues: 81.5449 Evaluate side-chains 224 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 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 = 0.3849 r_free = 0.3849 target = 0.129209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099999 restraints weight = 35360.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102903 restraints weight = 31819.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103239 restraints weight = 26737.164| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15664 Z= 0.221 Angle : 0.663 9.770 21198 Z= 0.331 Chirality : 0.045 0.544 2400 Planarity : 0.004 0.060 2659 Dihedral : 6.298 59.494 2324 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.66 % Allowed : 21.74 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1909 helix: 0.98 (0.19), residues: 830 sheet: -1.19 (0.49), residues: 119 loop : -2.66 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 613 HIS 0.002 0.000 HIS C 508 PHE 0.024 0.001 PHE D 555 TYR 0.031 0.001 TYR C 682 ARG 0.002 0.000 ARG E 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.87 seconds wall clock time: 51 minutes 15.90 seconds (3075.90 seconds total)