Starting phenix.real_space_refine on Wed Nov 15 17:33:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/11_2023/7s8v_24927_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/11_2023/7s8v_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_24927/11_2023/7s8v_24927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/11_2023/7s8v_24927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/11_2023/7s8v_24927_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8v_24927/11_2023/7s8v_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-1.21rc1-5144/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 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 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 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 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 chiralities: 4 Time building chain proxies: 6.11, per 1000 atoms: 0.49 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: 10.39 Conformation dependent library (CDL) restraints added in 1.4 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: 1.31 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: 4.78 Time building geometry restraints manager: 10.69 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 - 17.67: 4707 17.67 - 35.34: 335 35.34 - 53.02: 64 53.02 - 70.69: 10 70.69 - 88.36: 7 Dihedral angle restraints: 5123 sinusoidal: 2382 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 5120 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: 5.340 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: 0.210 Extract box with map and model: 13.970 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 44.350 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.250 ------------------------------------------------------------------------------- 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 : 12.458 88.358 2414 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 *********************** 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 : 1.043 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 outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.5644 time to fit residues: 90.9391 Evaluate side-chains 88 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3226 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.6805 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6620 Z= 0.308 Angle : 0.727 12.189 8986 Z= 0.369 Chirality : 0.046 0.156 993 Planarity : 0.005 0.085 1160 Dihedral : 4.635 22.330 860 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.13 % Allowed : 11.14 % Favored : 87.73 % 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: -2.99 (0.28), residues: 768 helix: -3.22 (0.48), residues: 63 sheet: -1.39 (0.33), residues: 231 loop : -2.19 (0.26), residues: 474 *********************** 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 100 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.5066 time to fit residues: 62.7757 Evaluate side-chains 81 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2751 time to fit residues: 3.2900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 870 ASN B 148 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6620 Z= 0.239 Angle : 0.663 10.505 8986 Z= 0.335 Chirality : 0.046 0.248 993 Planarity : 0.005 0.083 1160 Dihedral : 4.878 23.464 860 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.99 % Allowed : 12.27 % Favored : 86.74 % 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: -2.79 (0.28), residues: 768 helix: -2.81 (0.51), residues: 63 sheet: -1.21 (0.33), residues: 234 loop : -2.13 (0.26), residues: 471 *********************** 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 81 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.135 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 outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.4702 time to fit residues: 46.9675 Evaluate side-chains 73 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1622 time to fit residues: 2.4913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6620 Z= 0.269 Angle : 0.654 7.717 8986 Z= 0.338 Chirality : 0.045 0.183 993 Planarity : 0.005 0.086 1160 Dihedral : 4.818 19.164 860 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.99 % Allowed : 12.83 % Favored : 86.18 % 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: -2.70 (0.28), residues: 768 helix: -2.61 (0.51), residues: 63 sheet: -1.18 (0.34), residues: 218 loop : -2.05 (0.26), residues: 487 *********************** 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 79 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.048 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 outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.4845 time to fit residues: 47.7470 Evaluate side-chains 72 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1769 time to fit residues: 3.0248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7139 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6620 Z= 0.301 Angle : 0.709 14.070 8986 Z= 0.361 Chirality : 0.046 0.186 993 Planarity : 0.006 0.086 1160 Dihedral : 5.045 20.547 860 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 1.41 % Allowed : 15.09 % 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: -2.67 (0.28), residues: 768 helix: -2.14 (0.58), residues: 63 sheet: -1.15 (0.34), residues: 213 loop : -2.10 (0.27), residues: 492 *********************** 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 76 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.014 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 outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.4825 time to fit residues: 45.9173 Evaluate side-chains 63 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1497 time to fit residues: 2.6552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6620 Z= 0.318 Angle : 0.701 10.371 8986 Z= 0.361 Chirality : 0.046 0.193 993 Planarity : 0.006 0.087 1160 Dihedral : 5.315 22.757 860 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.26 % Allowed : 16.50 % 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: -2.76 (0.28), residues: 768 helix: -2.21 (0.58), residues: 63 sheet: -1.25 (0.35), residues: 213 loop : -2.15 (0.26), residues: 492 *********************** 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 80 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.031 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 outliers start: 16 outliers final: 9 residues processed: 74 average time/residue: 0.4336 time to fit residues: 42.5750 Evaluate side-chains 69 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1755 time to fit residues: 4.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7196 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6620 Z= 0.183 Angle : 0.615 6.896 8986 Z= 0.311 Chirality : 0.045 0.160 993 Planarity : 0.005 0.099 1160 Dihedral : 5.060 20.125 860 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 16.64 % Favored : 83.36 % 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: -2.48 (0.29), residues: 768 helix: -2.03 (0.57), residues: 63 sheet: -0.97 (0.36), residues: 212 loop : -1.99 (0.27), residues: 493 *********************** 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 62 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.139 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 outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4473 time to fit residues: 36.7129 Evaluate side-chains 59 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 827 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: 0.7274 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6620 Z= 0.288 Angle : 0.648 5.868 8986 Z= 0.333 Chirality : 0.045 0.203 993 Planarity : 0.005 0.087 1160 Dihedral : 5.191 19.917 860 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.42 % Allowed : 17.49 % 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: -2.53 (0.29), residues: 768 helix: -1.98 (0.59), residues: 63 sheet: -1.08 (0.35), residues: 210 loop : -1.99 (0.27), residues: 495 *********************** 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 67 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 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 outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.4657 time to fit residues: 40.8662 Evaluate side-chains 59 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7261 moved from start: 0.7266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6620 Z= 0.204 Angle : 0.613 5.686 8986 Z= 0.311 Chirality : 0.045 0.155 993 Planarity : 0.005 0.089 1160 Dihedral : 5.077 19.556 860 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.42 % Allowed : 17.77 % Favored : 81.81 % 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: -1.94 (0.57), residues: 63 sheet: -0.88 (0.37), residues: 198 loop : -1.92 (0.27), residues: 507 *********************** 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 63 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.102 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 outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.4527 time to fit residues: 36.6921 Evaluate side-chains 58 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1430 time to fit residues: 1.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 76 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 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: 0.7247 moved from start: 0.7415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6620 Z= 0.169 Angle : 0.587 5.665 8986 Z= 0.299 Chirality : 0.045 0.156 993 Planarity : 0.005 0.088 1160 Dihedral : 4.888 18.431 860 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % 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: -2.20 (0.29), residues: 768 helix: -1.86 (0.58), residues: 64 sheet: -0.73 (0.37), residues: 208 loop : -1.81 (0.27), residues: 496 ********************** 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 58 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.062 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 outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.4725 time to fit residues: 36.6442 Evaluate side-chains 53 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.080822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.068075 restraints weight = 99540.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.069944 restraints weight = 52485.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.071083 restraints weight = 33655.648| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6620 Z= 0.212 Angle : 0.597 6.483 8986 Z= 0.306 Chirality : 0.044 0.173 993 Planarity : 0.005 0.092 1160 Dihedral : 4.880 17.961 860 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 18.48 % 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: -2.21 (0.30), residues: 768 helix: -1.80 (0.58), residues: 64 sheet: -0.77 (0.37), residues: 208 loop : -1.81 (0.27), residues: 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.74 seconds wall clock time: 61 minutes 14.50 seconds (3674.50 seconds total)