Starting phenix.real_space_refine on Fri Jan 19 20:42:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/01_2024/7s8v_24927_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/01_2024/7s8v_24927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/01_2024/7s8v_24927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/01_2024/7s8v_24927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/01_2024/7s8v_24927_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/01_2024/7s8v_24927_trim.pdb" } resolution = 3.73 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= 0.011 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 S 48 5.16 5 C 4070 2.51 5 N 1102 2.21 5 O 1237 1.98 5 H 6045 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B ASP 801": "OD1" <-> "OD2" Residue "B GLU 833": "OE1" <-> "OE2" Residue "B GLU 867": "OE1" <-> "OE2" Residue "B ASP 922": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12502 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4190 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 22, 'TRANS': 241} Chain breaks: 2 Chain: "B" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 8147 Classifications: {'peptide': 518} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 485} Chain breaks: 3 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: 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: "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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.96, per 1000 atoms: 0.48 Number of scatterers: 12502 At special positions: 0 Unit cell: (95.4, 118.72, 106, 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) S 48 16.00 O 1237 8.00 N 1102 7.00 C 4070 6.00 H 6045 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.04 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A6101 " - " ASN A 610 " " NAG B1601 " - " ASN B 16 " " NAG B1602 " - " ASN B 25 " " NAG B1603 " - " ASN B 624 " " NAG B1604 " - " ASN B 606 " " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN B 111 " " NAG E 1 " - " ASN B 215 " Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 11.8% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.700A pdb=" N ASP A 649 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 684 Processing helix chain 'A' and resid 686 through 698 Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.139A pdb=" N ARG A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 852 through 857' Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.656A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.730A pdb=" N CYS B 196 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.537A pdb=" N HIS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 874 through 881 removed outlier: 3.729A pdb=" N PHE B 878 " --> pdb=" O SER B 874 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 590 removed outlier: 5.340A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.533A pdb=" N HIS A 774 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.061A pdb=" N THR A 872 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.061A pdb=" N THR A 872 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 14 removed outlier: 4.579A pdb=" N VAL B 7 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 30 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER B 27 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 82 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 14 removed outlier: 4.579A pdb=" N VAL B 7 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 30 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N LEU B 62 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 94 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLU B 120 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B 96 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN B 122 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 144 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 146 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.573A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.718A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 5.990A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AB4, first strand: chain 'B' and resid 599 through 604 removed outlier: 5.381A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 771 through 774 Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 832 removed outlier: 5.291A pdb=" N GLN B 845 " --> pdb=" O PRO B 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 869 through 873 removed outlier: 3.627A pdb=" N LEU B 856 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 901 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 898 " --> pdb=" O TRP B 909 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP B 909 " --> pdb=" O ILE B 898 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 900 " --> pdb=" O GLY B 907 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 869 through 873 removed outlier: 3.627A pdb=" N LEU B 856 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 901 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 894 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 915 " --> pdb=" O TYR B 894 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 474 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: 4.38 Time building geometry restraints manager: 10.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6041 1.04 - 1.24: 693 1.24 - 1.44: 2206 1.44 - 1.64: 3667 1.64 - 1.84: 58 Bond restraints: 12665 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 NAG A6101 " pdb=" O5 NAG A6101 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG B1601 " pdb=" O5 NAG B1601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" C1 NAG B1604 " pdb=" O5 NAG B1604 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 12660 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.53: 275 106.53 - 113.39: 14575 113.39 - 120.26: 4038 120.26 - 127.12: 3795 127.12 - 133.98: 97 Bond angle restraints: 22780 Sorted by residual: angle pdb=" CA CYS B 288 " pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " ideal model delta sigma weight residual 114.40 121.39 -6.99 2.30e+00 1.89e-01 9.24e+00 angle pdb=" N CYS B 288 " pdb=" CA CYS B 288 " pdb=" CB CYS B 288 " ideal model delta sigma weight residual 110.14 114.02 -3.88 1.41e+00 5.03e-01 7.56e+00 angle pdb=" C LEU B 599 " pdb=" N ASP B 600 " pdb=" CA ASP B 600 " ideal model delta sigma weight residual 121.80 128.06 -6.26 2.44e+00 1.68e-01 6.58e+00 angle pdb=" CA CYS B 301 " pdb=" CB CYS B 301 " pdb=" SG CYS B 301 " ideal model delta sigma weight residual 114.40 109.02 5.38 2.30e+00 1.89e-01 5.48e+00 angle pdb=" C CYS B 288 " pdb=" CA CYS B 288 " pdb=" CB CYS B 288 " ideal model delta sigma weight residual 109.26 112.58 -3.32 1.47e+00 4.63e-01 5.11e+00 ... (remaining 22775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 5771 21.93 - 43.86: 322 43.86 - 65.80: 56 65.80 - 87.73: 14 87.73 - 109.66: 5 Dihedral angle restraints: 6168 sinusoidal: 3427 harmonic: 2741 Sorted by residual: dihedral pdb=" CA LEU B 305 " pdb=" C LEU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 149.11 30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CB CYS B 8 " pdb=" SG CYS B 8 " pdb=" SG CYS B 26 " pdb=" CB CYS B 26 " ideal model delta sinusoidal sigma weight residual 93.00 143.03 -50.03 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS B 798 " pdb=" SG CYS B 798 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual 93.00 46.02 46.98 1 1.00e+01 1.00e-02 3.05e+01 ... (remaining 6165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 990 0.330 - 0.661: 0 0.661 - 0.991: 0 0.991 - 1.322: 1 1.322 - 1.652: 2 Chirality restraints: 993 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-02 2.50e+03 6.82e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.61e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-02 2.50e+03 3.01e+03 ... (remaining 990 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 306 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO B 307 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 842 " 0.004 2.00e-02 2.50e+03 1.15e-02 1.98e+00 pdb=" CD GLN A 842 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 842 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A 842 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 842 " 0.007 2.00e-02 2.50e+03 pdb="HE22 GLN A 842 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 616 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO B 617 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.017 5.00e-02 4.00e+02 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 608 2.15 - 2.76: 23669 2.76 - 3.37: 34404 3.37 - 3.99: 45992 3.99 - 4.60: 69424 Nonbonded interactions: 174097 Sorted by model distance: nonbonded pdb=" H PHE A 766 " pdb=" OG1 THR A 795 " model vdw 1.535 1.850 nonbonded pdb="HE21 GLN A 876 " pdb=" O GLY A 884 " model vdw 1.545 1.850 nonbonded pdb=" O TRP A 822 " pdb=" HH TYR A 855 " model vdw 1.555 1.850 nonbonded pdb=" O ALA A 644 " pdb=" HG1 THR A 647 " model vdw 1.556 1.850 nonbonded pdb=" O CYS B 266 " pdb="HH11 ARG B 270 " model vdw 1.572 1.850 ... (remaining 174092 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 'C' selection = chain 'E' } 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: 4.420 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: 0.180 Extract box with map and model: 14.340 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 43.090 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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 0.043 6620 Z= 0.238 Angle : 0.646 6.991 8986 Z= 0.327 Chirality : 0.093 1.652 993 Planarity : 0.004 0.055 1160 Dihedral : 13.875 109.661 2664 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.48 (0.27), residues: 768 helix: -3.77 (0.47), residues: 54 sheet: -1.79 (0.32), residues: 216 loop : -2.50 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 822 HIS 0.003 0.001 HIS B 247 PHE 0.012 0.001 PHE B 51 TYR 0.011 0.001 TYR A 689 ARG 0.009 0.001 ARG B 806 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8520 (mt) cc_final: 0.8214 (mt) REVERT: A 602 ASN cc_start: 0.8309 (m-40) cc_final: 0.7727 (m110) REVERT: A 691 LYS cc_start: 0.9275 (tptt) cc_final: 0.8952 (tppt) REVERT: A 778 HIS cc_start: 0.6277 (m90) cc_final: 0.5981 (p90) REVERT: A 834 MET cc_start: 0.7055 (ptm) cc_final: 0.6665 (ptp) REVERT: B 90 ASN cc_start: 0.9082 (t0) cc_final: 0.8365 (t0) REVERT: B 110 MET cc_start: 0.6112 (mmt) cc_final: 0.5603 (mmt) REVERT: B 611 ILE cc_start: 0.8117 (mt) cc_final: 0.7774 (mt) REVERT: B 845 GLN cc_start: 0.8265 (tp40) cc_final: 0.6923 (mp10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.5473 time to fit residues: 88.3684 Evaluate side-chains 91 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 34 GLN B 123 ASN B 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6620 Z= 0.257 Angle : 0.680 7.225 8986 Z= 0.341 Chirality : 0.047 0.287 993 Planarity : 0.005 0.086 1160 Dihedral : 9.444 64.127 1110 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.27 % Allowed : 10.44 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.28), residues: 768 helix: -3.16 (0.50), residues: 62 sheet: -1.38 (0.32), residues: 231 loop : -2.14 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 618 HIS 0.007 0.001 HIS B 280 PHE 0.012 0.002 PHE B 89 TYR 0.018 0.002 TYR A 689 ARG 0.008 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASN cc_start: 0.8232 (m-40) cc_final: 0.7984 (m110) REVERT: A 691 LYS cc_start: 0.9259 (tptt) cc_final: 0.9024 (tppt) REVERT: A 778 HIS cc_start: 0.6681 (m90) cc_final: 0.6281 (p-80) REVERT: A 834 MET cc_start: 0.7561 (ptm) cc_final: 0.6987 (ptp) REVERT: B 34 GLN cc_start: 0.7118 (mt0) cc_final: 0.6683 (mp10) REVERT: B 90 ASN cc_start: 0.8950 (t0) cc_final: 0.8727 (t0) REVERT: B 845 GLN cc_start: 0.8307 (tp40) cc_final: 0.6984 (mp10) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.4892 time to fit residues: 62.3207 Evaluate side-chains 87 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 614 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A 870 ASN B 148 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6620 Z= 0.325 Angle : 0.704 6.389 8986 Z= 0.365 Chirality : 0.047 0.283 993 Planarity : 0.007 0.109 1160 Dihedral : 7.569 53.781 1110 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.83 % Allowed : 11.57 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.28), residues: 768 helix: -2.88 (0.49), residues: 62 sheet: -1.26 (0.33), residues: 225 loop : -2.19 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.012 0.002 HIS A 630 PHE 0.022 0.002 PHE A 747 TYR 0.019 0.002 TYR A 689 ARG 0.004 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LYS cc_start: 0.9304 (tptt) cc_final: 0.9102 (tppt) REVERT: A 778 HIS cc_start: 0.6945 (m90) cc_final: 0.6720 (p90) REVERT: A 834 MET cc_start: 0.8023 (ptm) cc_final: 0.7486 (ptp) REVERT: B 13 ILE cc_start: 0.8132 (mp) cc_final: 0.7908 (mp) REVERT: B 90 ASN cc_start: 0.9054 (t0) cc_final: 0.8710 (t0) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.4600 time to fit residues: 48.9115 Evaluate side-chains 79 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 0.0270 chunk 36 optimal weight: 0.0670 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6620 Z= 0.233 Angle : 0.602 5.615 8986 Z= 0.308 Chirality : 0.045 0.171 993 Planarity : 0.005 0.087 1160 Dihedral : 6.888 58.562 1110 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.69 % Allowed : 12.55 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.28), residues: 768 helix: -2.47 (0.54), residues: 62 sheet: -1.04 (0.34), residues: 217 loop : -2.05 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 618 HIS 0.006 0.001 HIS B 275 PHE 0.010 0.002 PHE B 631 TYR 0.015 0.001 TYR A 689 ARG 0.007 0.000 ARG B 882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.6997 (m90) cc_final: 0.6661 (p90) REVERT: A 834 MET cc_start: 0.8122 (ptm) cc_final: 0.7600 (ptp) REVERT: B 90 ASN cc_start: 0.9096 (t0) cc_final: 0.8851 (t0) REVERT: B 97 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7480 (mm-30) REVERT: B 287 GLU cc_start: 0.8217 (mp0) cc_final: 0.6801 (tp30) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.4583 time to fit residues: 47.9750 Evaluate side-chains 76 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6620 Z= 0.200 Angle : 0.583 8.317 8986 Z= 0.296 Chirality : 0.044 0.174 993 Planarity : 0.005 0.086 1160 Dihedral : 6.229 58.882 1110 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 1.55 % Allowed : 13.26 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.29), residues: 768 helix: -2.32 (0.54), residues: 63 sheet: -0.85 (0.35), residues: 223 loop : -1.91 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 618 HIS 0.003 0.001 HIS B 247 PHE 0.011 0.001 PHE B 96 TYR 0.013 0.001 TYR A 689 ARG 0.004 0.000 ARG B 882 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.7086 (m90) cc_final: 0.6755 (p90) REVERT: A 834 MET cc_start: 0.8176 (ptm) cc_final: 0.7674 (ptp) REVERT: B 90 ASN cc_start: 0.9161 (t0) cc_final: 0.8690 (t0) REVERT: B 97 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 800 GLN cc_start: 0.5674 (OUTLIER) cc_final: 0.4781 (tt0) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.4053 time to fit residues: 41.1637 Evaluate side-chains 76 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 800 GLN Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 6620 Z= 0.358 Angle : 0.715 6.041 8986 Z= 0.370 Chirality : 0.047 0.183 993 Planarity : 0.006 0.086 1160 Dihedral : 7.118 53.598 1110 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 2.82 % Allowed : 13.68 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.29), residues: 768 helix: -2.13 (0.60), residues: 63 sheet: -1.26 (0.35), residues: 214 loop : -2.21 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 183 HIS 0.007 0.001 HIS B 247 PHE 0.015 0.002 PHE B 51 TYR 0.023 0.002 TYR A 689 ARG 0.007 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.7195 (m90) cc_final: 0.6982 (p90) REVERT: A 796 MET cc_start: 0.8079 (tpp) cc_final: 0.7710 (tpp) REVERT: A 834 MET cc_start: 0.8566 (ptm) cc_final: 0.8001 (ptp) REVERT: A 893 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.4077 (m-10) REVERT: B 90 ASN cc_start: 0.9265 (t0) cc_final: 0.8798 (t0) REVERT: B 97 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 120 GLU cc_start: 0.8027 (tt0) cc_final: 0.7713 (tt0) REVERT: B 304 CYS cc_start: 0.3595 (OUTLIER) cc_final: 0.3147 (p) REVERT: B 800 GLN cc_start: 0.5976 (OUTLIER) cc_final: 0.5195 (tt0) REVERT: B 844 TRP cc_start: 0.3906 (p90) cc_final: 0.2850 (p90) outliers start: 20 outliers final: 16 residues processed: 82 average time/residue: 0.4054 time to fit residues: 44.3352 Evaluate side-chains 79 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 800 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6620 Z= 0.238 Angle : 0.622 5.592 8986 Z= 0.319 Chirality : 0.045 0.157 993 Planarity : 0.005 0.086 1160 Dihedral : 6.674 46.801 1110 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.40 % Allowed : 15.51 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.29), residues: 768 helix: -2.09 (0.58), residues: 63 sheet: -1.00 (0.36), residues: 217 loop : -2.10 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 810 HIS 0.005 0.001 HIS B 247 PHE 0.021 0.002 PHE B 231 TYR 0.014 0.001 TYR A 689 ARG 0.008 0.001 ARG B 882 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8623 (ptm) cc_final: 0.8086 (ptp) REVERT: A 893 TYR cc_start: 0.5174 (OUTLIER) cc_final: 0.4432 (m-10) REVERT: B 90 ASN cc_start: 0.9212 (t0) cc_final: 0.8721 (t0) REVERT: B 97 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 304 CYS cc_start: 0.3348 (OUTLIER) cc_final: 0.2866 (p) REVERT: B 800 GLN cc_start: 0.5975 (OUTLIER) cc_final: 0.5183 (tt0) outliers start: 17 outliers final: 14 residues processed: 76 average time/residue: 0.4603 time to fit residues: 46.8869 Evaluate side-chains 79 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 800 GLN Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6620 Z= 0.298 Angle : 0.655 5.977 8986 Z= 0.339 Chirality : 0.045 0.171 993 Planarity : 0.006 0.085 1160 Dihedral : 6.792 49.839 1110 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.68 % Allowed : 16.08 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.29), residues: 768 helix: -2.02 (0.60), residues: 63 sheet: -0.95 (0.36), residues: 208 loop : -2.05 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.006 0.001 HIS B 841 PHE 0.028 0.002 PHE B 231 TYR 0.018 0.002 TYR A 689 ARG 0.011 0.001 ARG B 882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8771 (ptm) cc_final: 0.8262 (ptp) REVERT: A 893 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4608 (m-10) REVERT: B 90 ASN cc_start: 0.9289 (t0) cc_final: 0.8811 (t0) REVERT: B 97 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7882 (mm-30) REVERT: B 304 CYS cc_start: 0.3822 (OUTLIER) cc_final: 0.3374 (p) REVERT: B 800 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5480 (tt0) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.4499 time to fit residues: 46.2237 Evaluate side-chains 77 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 800 GLN Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6620 Z= 0.202 Angle : 0.609 8.866 8986 Z= 0.312 Chirality : 0.045 0.159 993 Planarity : 0.005 0.083 1160 Dihedral : 6.392 44.667 1110 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 1.97 % Allowed : 16.64 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.29), residues: 768 helix: -1.94 (0.58), residues: 64 sheet: -0.82 (0.36), residues: 212 loop : -1.92 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 632 HIS 0.013 0.001 HIS B 247 PHE 0.015 0.002 PHE B 231 TYR 0.012 0.001 TYR A 689 ARG 0.009 0.001 ARG B 882 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8750 (ptm) cc_final: 0.8242 (ptp) REVERT: A 893 TYR cc_start: 0.5362 (OUTLIER) cc_final: 0.4664 (m-10) REVERT: B 90 ASN cc_start: 0.9254 (t0) cc_final: 0.8770 (t0) REVERT: B 97 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 304 CYS cc_start: 0.3536 (OUTLIER) cc_final: 0.3100 (p) REVERT: B 800 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5513 (tt0) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.4475 time to fit residues: 43.3215 Evaluate side-chains 71 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 800 GLN Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.7541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6620 Z= 0.188 Angle : 0.596 6.429 8986 Z= 0.305 Chirality : 0.044 0.162 993 Planarity : 0.005 0.085 1160 Dihedral : 5.964 36.218 1110 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 1.83 % Allowed : 16.64 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.30), residues: 768 helix: -1.87 (0.59), residues: 64 sheet: -0.73 (0.37), residues: 212 loop : -1.81 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 632 HIS 0.012 0.001 HIS B 247 PHE 0.018 0.001 PHE B 231 TYR 0.011 0.001 TYR A 689 ARG 0.009 0.000 ARG B 882 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8790 (ptm) cc_final: 0.8259 (ptp) REVERT: A 841 SER cc_start: 0.7545 (p) cc_final: 0.7334 (p) REVERT: A 891 PHE cc_start: 0.6230 (p90) cc_final: 0.6020 (p90) REVERT: A 893 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.4716 (m-10) REVERT: B 90 ASN cc_start: 0.9289 (t0) cc_final: 0.8809 (t0) REVERT: B 97 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7849 (mm-30) REVERT: B 304 CYS cc_start: 0.3569 (OUTLIER) cc_final: 0.3151 (p) REVERT: B 800 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5437 (tt0) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.4474 time to fit residues: 40.9412 Evaluate side-chains 72 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 800 GLN Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.080868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.068013 restraints weight = 102399.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.069993 restraints weight = 52950.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.071153 restraints weight = 33315.122| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6620 Z= 0.183 Angle : 0.584 6.306 8986 Z= 0.298 Chirality : 0.044 0.161 993 Planarity : 0.005 0.086 1160 Dihedral : 5.740 33.039 1110 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 1.83 % Allowed : 16.78 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.30), residues: 768 helix: -1.80 (0.60), residues: 64 sheet: -0.64 (0.37), residues: 212 loop : -1.76 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 632 HIS 0.013 0.001 HIS B 247 PHE 0.017 0.001 PHE B 231 TYR 0.012 0.001 TYR A 689 ARG 0.008 0.000 ARG B 882 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.73 seconds wall clock time: 66 minutes 3.11 seconds (3963.11 seconds total)