Starting phenix.real_space_refine on Wed May 8 21:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/05_2024/8wor_37696_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/05_2024/8wor_37696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/05_2024/8wor_37696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/05_2024/8wor_37696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/05_2024/8wor_37696_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/05_2024/8wor_37696_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 S 60 5.16 5 C 7539 2.51 5 N 1696 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11218 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 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: 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: "E" 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: "F" 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: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.93, per 1000 atoms: 0.97 Number of scatterers: 11218 At special positions: 0 Unit cell: (93.61, 89.355, 135.309, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 60 16.00 O 1919 8.00 N 1696 7.00 C 7539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 787 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 903 " - " ASN A 67 " " NAG A 904 " - " ASN A 136 " " NAG B 903 " - " ASN B 67 " " NAG B 904 " - " ASN B 136 " " NAG C 1 " - " ASN A 57 " " NAG D 1 " - " ASN A 83 " " NAG E 1 " - " ASN B 57 " " NAG F 1 " - " ASN B 83 " Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 46.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.842A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 473 removed outlier: 4.024A pdb=" N ILE A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 495 through 526 removed outlier: 4.874A pdb=" N ASN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 564 removed outlier: 3.635A pdb=" N VAL A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 593 removed outlier: 3.790A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 620 Processing helix chain 'A' and resid 625 through 649 removed outlier: 3.852A pdb=" N PHE A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 708 Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'A' and resid 746 through 767 removed outlier: 3.597A pdb=" N PHE A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 783 removed outlier: 3.935A pdb=" N LYS A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 795 through 815 Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 303 through 334 removed outlier: 3.841A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 473 removed outlier: 4.014A pdb=" N ILE B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 495 through 526 removed outlier: 4.832A pdb=" N ASN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 564 removed outlier: 3.630A pdb=" N VAL B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 593 removed outlier: 3.785A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 620 Processing helix chain 'B' and resid 625 through 649 removed outlier: 4.545A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 708 Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'B' and resid 746 through 767 removed outlier: 3.625A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 783 removed outlier: 3.936A pdb=" N LYS B 783 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 795 through 815 Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing sheet with id= A, first strand: chain 'A' and resid 50 through 56 removed outlier: 4.517A pdb=" N HIS A 50 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 163 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 61 through 70 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 113 Processing sheet with id= D, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= E, first strand: chain 'A' and resid 187 through 192 Processing sheet with id= F, first strand: chain 'B' and resid 50 through 56 removed outlier: 4.531A pdb=" N HIS B 50 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 163 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA B 77 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 61 through 70 Processing sheet with id= H, first strand: chain 'B' and resid 110 through 113 Processing sheet with id= I, first strand: chain 'B' and resid 177 through 181 Processing sheet with id= J, first strand: chain 'B' and resid 187 through 192 592 hydrogen bonds defined for protein. 1654 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: 3.46 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3258 1.34 - 1.46: 2819 1.46 - 1.58: 5368 1.58 - 1.70: 2 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: bond pdb=" C10 OLA A 911 " pdb=" C9 OLA A 911 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C10 OLA B 914 " pdb=" C9 OLA B 914 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" CB PRO B 748 " pdb=" CG PRO B 748 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.79e+00 bond pdb=" CB PRO A 748 " pdb=" CG PRO A 748 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.43e+00 bond pdb=" C1 OLA A 911 " pdb=" C2 OLA A 911 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 97.20 - 105.30: 253 105.30 - 113.40: 6546 113.40 - 121.51: 6525 121.51 - 129.61: 2362 129.61 - 137.71: 62 Bond angle restraints: 15748 Sorted by residual: angle pdb=" CA LEU B 728 " pdb=" CB LEU B 728 " pdb=" CG LEU B 728 " ideal model delta sigma weight residual 116.30 137.71 -21.41 3.50e+00 8.16e-02 3.74e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 104.60 7.40 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 134.47 -18.17 3.50e+00 8.16e-02 2.70e+01 angle pdb=" CA PRO A 748 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C ILE B 612 " pdb=" N MET B 613 " pdb=" CA MET B 613 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.67e+00 3.59e-01 1.54e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6563 17.36 - 34.73: 800 34.73 - 52.09: 223 52.09 - 69.45: 57 69.45 - 86.82: 8 Dihedral angle restraints: 7651 sinusoidal: 3791 harmonic: 3860 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual 0.00 20.33 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 0.00 20.20 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA CYS A 787 " pdb=" C CYS A 787 " pdb=" N ILE A 788 " pdb=" CA ILE A 788 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1583 0.057 - 0.115: 232 0.115 - 0.172: 21 0.172 - 0.229: 2 0.229 - 0.287: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA MET A 613 " pdb=" N MET A 613 " pdb=" C MET A 613 " pdb=" CB MET A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 911 " -0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA A 911 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 911 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 911 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA B 914 " -0.085 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.085 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO A 748 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " 0.065 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 61 2.52 - 3.12: 8615 3.12 - 3.71: 16147 3.71 - 4.31: 23030 4.31 - 4.90: 39565 Nonbonded interactions: 87418 Sorted by model distance: nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1001 " model vdw 1.928 2.230 nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1001 " model vdw 1.928 2.230 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.080 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.085 2.440 nonbonded pdb=" O ASN B 598 " pdb=" OH TYR B 602 " model vdw 2.193 2.440 ... (remaining 87413 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 35 through 80 or resid 82 through 830 or resid 901 through \ 906 or resid 908 through 910 or resid 913)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 906 or resid 908 through 910 or resid 913)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.21 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: 1.980 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: 10.030 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 41.560 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 0.136 11541 Z= 0.243 Angle : 0.636 21.410 15748 Z= 0.307 Chirality : 0.041 0.287 1840 Planarity : 0.007 0.144 1850 Dihedral : 15.745 86.815 5135 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 5.08 % Allowed : 27.19 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.24), residues: 1276 helix: 2.90 (0.21), residues: 590 sheet: 1.34 (0.30), residues: 272 loop : -2.08 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 PHE 0.038 0.001 PHE A 732 TYR 0.011 0.001 TYR B 188 ARG 0.001 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8744 (mp10) REVERT: A 158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8296 (mt0) REVERT: A 554 MET cc_start: 0.7669 (tpp) cc_final: 0.7331 (mmm) REVERT: B 117 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8797 (mp10) REVERT: B 554 MET cc_start: 0.7676 (tpp) cc_final: 0.7338 (mmm) REVERT: B 650 MET cc_start: 0.2997 (tpt) cc_final: 0.2770 (tpt) REVERT: B 686 MET cc_start: 0.5258 (mmt) cc_final: 0.4300 (pmm) REVERT: B 718 MET cc_start: 0.8145 (ttp) cc_final: 0.7940 (ttm) outliers start: 59 outliers final: 47 residues processed: 170 average time/residue: 0.8481 time to fit residues: 161.3564 Evaluate side-chains 160 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 0.0030 chunk 116 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 142 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11541 Z= 0.182 Angle : 0.694 18.479 15748 Z= 0.324 Chirality : 0.044 0.293 1840 Planarity : 0.005 0.075 1850 Dihedral : 9.660 59.239 2800 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.53 % Rotamer: Outliers : 5.08 % Allowed : 25.73 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.14 (0.21), residues: 606 sheet: 1.47 (0.28), residues: 276 loop : -1.93 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.008 0.001 HIS B 636 PHE 0.016 0.001 PHE A 722 TYR 0.013 0.001 TYR B 188 ARG 0.004 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 117 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8335 (mm-40) REVERT: A 158 GLN cc_start: 0.8533 (mt0) cc_final: 0.8304 (mt0) REVERT: A 554 MET cc_start: 0.7482 (tpp) cc_final: 0.7144 (mmm) REVERT: A 594 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.6114 (m90) REVERT: A 650 MET cc_start: 0.3807 (OUTLIER) cc_final: 0.3555 (mmt) REVERT: A 686 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.3214 (ttt) REVERT: A 736 MET cc_start: 0.7134 (tmm) cc_final: 0.6893 (mmm) REVERT: B 117 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8820 (mp10) REVERT: B 207 GLU cc_start: 0.7214 (mp0) cc_final: 0.7013 (mp0) REVERT: B 554 MET cc_start: 0.7501 (tpp) cc_final: 0.7154 (mmm) REVERT: B 605 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.3529 (p90) REVERT: B 650 MET cc_start: 0.2965 (tpt) cc_final: 0.2754 (tpt) REVERT: B 686 MET cc_start: 0.5123 (OUTLIER) cc_final: 0.4092 (pmm) REVERT: B 712 ARG cc_start: 0.4988 (mpt180) cc_final: 0.3998 (mpp80) outliers start: 59 outliers final: 28 residues processed: 163 average time/residue: 0.9278 time to fit residues: 169.2406 Evaluate side-chains 142 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11541 Z= 0.320 Angle : 0.713 18.599 15748 Z= 0.344 Chirality : 0.046 0.274 1840 Planarity : 0.005 0.068 1850 Dihedral : 8.866 58.716 2757 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 5.51 % Allowed : 26.33 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.02 (0.23), residues: 1276 helix: 2.02 (0.21), residues: 590 sheet: 1.46 (0.28), residues: 274 loop : -2.02 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 627 HIS 0.006 0.001 HIS B 636 PHE 0.014 0.002 PHE A 722 TYR 0.016 0.002 TYR B 188 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 107 time to evaluate : 1.214 Fit side-chains REVERT: A 158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8302 (mt0) REVERT: A 554 MET cc_start: 0.7565 (tpp) cc_final: 0.7262 (mmm) REVERT: A 686 MET cc_start: 0.5205 (OUTLIER) cc_final: 0.3267 (ttt) REVERT: A 736 MET cc_start: 0.7154 (tmm) cc_final: 0.6859 (mmm) REVERT: B 117 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8839 (mp10) REVERT: B 554 MET cc_start: 0.7614 (tpp) cc_final: 0.7318 (mmm) REVERT: B 650 MET cc_start: 0.2992 (tpt) cc_final: 0.2776 (tpt) REVERT: B 686 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4036 (pmm) REVERT: B 712 ARG cc_start: 0.5018 (mpt180) cc_final: 0.4181 (mpp80) REVERT: B 718 MET cc_start: 0.8110 (mtm) cc_final: 0.7908 (ttm) outliers start: 64 outliers final: 32 residues processed: 161 average time/residue: 0.7784 time to fit residues: 141.7582 Evaluate side-chains 145 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 90 ASN A 142 GLN A 725 ASN A 769 ASN B 71 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11541 Z= 0.184 Angle : 0.658 18.131 15748 Z= 0.311 Chirality : 0.043 0.285 1840 Planarity : 0.005 0.062 1850 Dihedral : 8.325 58.761 2755 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 4.04 % Allowed : 26.85 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.02 (0.23), residues: 1276 helix: 1.89 (0.21), residues: 604 sheet: 1.54 (0.28), residues: 274 loop : -2.00 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 627 HIS 0.005 0.001 HIS B 636 PHE 0.012 0.001 PHE A 732 TYR 0.013 0.001 TYR B 188 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 1.186 Fit side-chains REVERT: A 158 GLN cc_start: 0.8506 (mt0) cc_final: 0.8286 (mt0) REVERT: A 554 MET cc_start: 0.7542 (tpp) cc_final: 0.7263 (mmm) REVERT: A 613 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (pmm) REVERT: A 686 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.3249 (ttt) REVERT: A 736 MET cc_start: 0.7100 (tmm) cc_final: 0.6815 (tpp) REVERT: B 554 MET cc_start: 0.7571 (tpp) cc_final: 0.7293 (mmm) REVERT: B 650 MET cc_start: 0.2985 (tpt) cc_final: 0.2767 (tpt) REVERT: B 686 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4024 (pmm) REVERT: B 710 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7841 (mmt-90) REVERT: B 712 ARG cc_start: 0.5117 (mpt180) cc_final: 0.4466 (mpp80) REVERT: B 718 MET cc_start: 0.8063 (mtm) cc_final: 0.7847 (ttm) outliers start: 47 outliers final: 24 residues processed: 148 average time/residue: 0.8610 time to fit residues: 142.4704 Evaluate side-chains 135 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 123 GLN A 725 ASN A 769 ASN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11541 Z= 0.359 Angle : 0.714 18.463 15748 Z= 0.347 Chirality : 0.047 0.282 1840 Planarity : 0.005 0.063 1850 Dihedral : 8.374 59.998 2749 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 4.91 % Allowed : 26.33 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.90 (0.23), residues: 1276 helix: 1.89 (0.21), residues: 590 sheet: 1.49 (0.29), residues: 274 loop : -2.09 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 627 HIS 0.005 0.001 HIS B 636 PHE 0.015 0.002 PHE A 454 TYR 0.018 0.002 TYR A 188 ARG 0.003 0.000 ARG B 781 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 108 time to evaluate : 1.308 Fit side-chains REVERT: A 158 GLN cc_start: 0.8515 (mt0) cc_final: 0.8284 (mt0) REVERT: A 554 MET cc_start: 0.7592 (tpp) cc_final: 0.7323 (mmm) REVERT: A 613 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8457 (pmm) REVERT: A 686 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4258 (mpt) REVERT: A 736 MET cc_start: 0.7098 (tmm) cc_final: 0.6809 (tpp) REVERT: B 461 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: B 554 MET cc_start: 0.7628 (tpp) cc_final: 0.7366 (mmm) REVERT: B 559 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7848 (p) REVERT: B 650 MET cc_start: 0.3018 (tpt) cc_final: 0.2795 (tpt) REVERT: B 686 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4089 (pmm) REVERT: B 710 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7775 (mmt-90) REVERT: B 712 ARG cc_start: 0.5130 (mpt180) cc_final: 0.4517 (mpp80) REVERT: B 718 MET cc_start: 0.8111 (mtm) cc_final: 0.7882 (ttm) outliers start: 57 outliers final: 37 residues processed: 152 average time/residue: 0.8619 time to fit residues: 146.7540 Evaluate side-chains 150 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 90 ASN A 142 GLN A 725 ASN A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11541 Z= 0.265 Angle : 0.686 18.618 15748 Z= 0.329 Chirality : 0.045 0.282 1840 Planarity : 0.005 0.060 1850 Dihedral : 8.172 59.333 2747 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 4.65 % Allowed : 26.42 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.89 (0.23), residues: 1276 helix: 1.88 (0.21), residues: 588 sheet: 1.51 (0.29), residues: 274 loop : -2.10 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 PHE 0.016 0.001 PHE B 732 TYR 0.015 0.001 TYR B 188 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 110 time to evaluate : 1.217 Fit side-chains REVERT: A 158 GLN cc_start: 0.8510 (mt0) cc_final: 0.8274 (mt0) REVERT: A 554 MET cc_start: 0.7589 (tpp) cc_final: 0.7308 (mmm) REVERT: A 613 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8465 (pmm) REVERT: A 686 MET cc_start: 0.5128 (OUTLIER) cc_final: 0.3148 (ttt) REVERT: A 736 MET cc_start: 0.7090 (tmm) cc_final: 0.6803 (tpp) REVERT: B 461 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: B 554 MET cc_start: 0.7633 (tpp) cc_final: 0.7362 (mmm) REVERT: B 559 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 650 MET cc_start: 0.3064 (tpt) cc_final: 0.2850 (tpt) REVERT: B 686 MET cc_start: 0.5030 (OUTLIER) cc_final: 0.4047 (pmm) REVERT: B 710 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7760 (mmt-90) REVERT: B 712 ARG cc_start: 0.5110 (mpt180) cc_final: 0.4545 (mpp80) outliers start: 54 outliers final: 32 residues processed: 152 average time/residue: 0.8721 time to fit residues: 148.0911 Evaluate side-chains 146 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 288 GLN A 725 ASN A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11541 Z= 0.194 Angle : 0.649 17.569 15748 Z= 0.310 Chirality : 0.043 0.291 1840 Planarity : 0.005 0.058 1850 Dihedral : 7.782 59.027 2747 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 4.04 % Allowed : 27.19 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.90 (0.23), residues: 1276 helix: 1.80 (0.21), residues: 602 sheet: 1.56 (0.28), residues: 274 loop : -2.14 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 PHE 0.016 0.001 PHE B 732 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 111 time to evaluate : 1.215 Fit side-chains REVERT: A 554 MET cc_start: 0.7556 (tpp) cc_final: 0.7271 (mmm) REVERT: A 686 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.3038 (ttt) REVERT: A 736 MET cc_start: 0.7012 (tmm) cc_final: 0.6765 (tpp) REVERT: B 554 MET cc_start: 0.7560 (tpp) cc_final: 0.7270 (mmm) REVERT: B 559 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7900 (p) REVERT: B 650 MET cc_start: 0.3038 (tpt) cc_final: 0.2819 (tpt) REVERT: B 686 MET cc_start: 0.4957 (OUTLIER) cc_final: 0.3930 (pmm) REVERT: B 710 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7758 (mmt-90) REVERT: B 712 ARG cc_start: 0.5098 (mpt180) cc_final: 0.4604 (mpp80) REVERT: B 736 MET cc_start: 0.7793 (tpp) cc_final: 0.7000 (mpp) outliers start: 47 outliers final: 29 residues processed: 144 average time/residue: 0.8877 time to fit residues: 142.3997 Evaluate side-chains 138 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 90 ASN A 142 GLN A 288 GLN A 725 ASN A 769 ASN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11541 Z= 0.177 Angle : 0.643 16.824 15748 Z= 0.308 Chirality : 0.043 0.292 1840 Planarity : 0.005 0.058 1850 Dihedral : 7.461 57.834 2739 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.53 % Rotamer: Outliers : 3.87 % Allowed : 27.45 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.92 (0.23), residues: 1276 helix: 1.95 (0.21), residues: 588 sheet: 1.60 (0.28), residues: 274 loop : -2.24 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 PHE 0.016 0.001 PHE B 732 TYR 0.013 0.001 TYR A 188 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 110 time to evaluate : 1.284 Fit side-chains REVERT: A 554 MET cc_start: 0.7571 (tpp) cc_final: 0.7289 (mmm) REVERT: A 605 TYR cc_start: 0.3765 (OUTLIER) cc_final: 0.3546 (p90) REVERT: A 686 MET cc_start: 0.5038 (mmt) cc_final: 0.4192 (mpt) REVERT: A 736 MET cc_start: 0.6995 (tmm) cc_final: 0.6737 (tpp) REVERT: B 554 MET cc_start: 0.7591 (tpp) cc_final: 0.7322 (mmm) REVERT: B 686 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.3952 (pmm) REVERT: B 710 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7754 (mmt-90) REVERT: B 712 ARG cc_start: 0.5082 (mpt180) cc_final: 0.4612 (mpp80) REVERT: B 718 MET cc_start: 0.8075 (mtm) cc_final: 0.7850 (ttm) REVERT: B 736 MET cc_start: 0.7743 (tpp) cc_final: 0.6936 (mpp) outliers start: 45 outliers final: 33 residues processed: 146 average time/residue: 0.8613 time to fit residues: 140.7660 Evaluate side-chains 142 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 725 ASN A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11541 Z= 0.281 Angle : 0.681 16.886 15748 Z= 0.331 Chirality : 0.045 0.284 1840 Planarity : 0.005 0.059 1850 Dihedral : 7.473 58.022 2739 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 3.96 % Allowed : 27.28 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.85 (0.23), residues: 1276 helix: 1.89 (0.21), residues: 590 sheet: 1.55 (0.28), residues: 274 loop : -2.26 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 PHE 0.018 0.001 PHE B 732 TYR 0.017 0.001 TYR A 188 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.151 Fit side-chains REVERT: A 554 MET cc_start: 0.7579 (tpp) cc_final: 0.7323 (mmm) REVERT: A 605 TYR cc_start: 0.3640 (OUTLIER) cc_final: 0.3405 (p90) REVERT: A 686 MET cc_start: 0.4988 (mmt) cc_final: 0.4129 (mpt) REVERT: A 736 MET cc_start: 0.6994 (tmm) cc_final: 0.6696 (mmm) REVERT: B 554 MET cc_start: 0.7569 (tpp) cc_final: 0.7326 (mmm) REVERT: B 559 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 686 MET cc_start: 0.4971 (mmt) cc_final: 0.3954 (pmm) REVERT: B 710 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7748 (mmt-90) REVERT: B 712 ARG cc_start: 0.5091 (mpt180) cc_final: 0.4616 (mpp80) REVERT: B 736 MET cc_start: 0.7782 (tpp) cc_final: 0.6976 (mpp) outliers start: 46 outliers final: 38 residues processed: 146 average time/residue: 0.8874 time to fit residues: 145.4494 Evaluate side-chains 147 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 127 optimal weight: 0.0570 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 78 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 0.0870 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 725 ASN B 769 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 11541 Z= 0.385 Angle : 0.918 59.199 15748 Z= 0.504 Chirality : 0.046 0.474 1840 Planarity : 0.005 0.059 1850 Dihedral : 7.473 58.045 2739 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 3.70 % Allowed : 27.54 % Favored : 68.76 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.85 (0.23), residues: 1276 helix: 1.89 (0.21), residues: 590 sheet: 1.54 (0.28), residues: 274 loop : -2.27 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.004 0.001 HIS B 563 PHE 0.016 0.001 PHE B 732 TYR 0.017 0.001 TYR A 188 ARG 0.002 0.000 ARG A 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 107 time to evaluate : 1.222 Fit side-chains REVERT: A 554 MET cc_start: 0.7575 (tpp) cc_final: 0.7338 (mmm) REVERT: A 605 TYR cc_start: 0.3633 (OUTLIER) cc_final: 0.3408 (p90) REVERT: A 686 MET cc_start: 0.4987 (mmt) cc_final: 0.4128 (mpt) REVERT: A 736 MET cc_start: 0.6992 (tmm) cc_final: 0.6693 (mmm) REVERT: B 554 MET cc_start: 0.7555 (tpp) cc_final: 0.7309 (mmm) REVERT: B 559 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7847 (p) REVERT: B 686 MET cc_start: 0.4969 (mmt) cc_final: 0.3954 (pmm) REVERT: B 710 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7747 (mmt-90) REVERT: B 712 ARG cc_start: 0.5088 (mpt180) cc_final: 0.4618 (mpp80) REVERT: B 736 MET cc_start: 0.7778 (tpp) cc_final: 0.6975 (mpp) outliers start: 43 outliers final: 38 residues processed: 143 average time/residue: 0.9238 time to fit residues: 147.2916 Evaluate side-chains 146 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN A 769 ASN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 90 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102307 restraints weight = 16557.351| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.75 r_work: 0.3130 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 11541 Z= 0.385 Angle : 0.918 59.199 15748 Z= 0.504 Chirality : 0.046 0.474 1840 Planarity : 0.005 0.059 1850 Dihedral : 7.473 58.045 2739 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 3.61 % Allowed : 27.62 % Favored : 68.76 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.85 (0.23), residues: 1276 helix: 1.89 (0.21), residues: 590 sheet: 1.54 (0.28), residues: 274 loop : -2.27 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.004 0.001 HIS B 563 PHE 0.016 0.001 PHE B 732 TYR 0.017 0.001 TYR A 188 ARG 0.002 0.000 ARG A 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.79 seconds wall clock time: 66 minutes 13.02 seconds (3973.02 seconds total)