Starting phenix.real_space_refine on Tue Jul 29 23:51:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0z_50119/07_2025/9f0z_50119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0z_50119/07_2025/9f0z_50119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_2025/9f0z_50119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_2025/9f0z_50119.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_2025/9f0z_50119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_2025/9f0z_50119.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 181 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 6919 2.51 5 N 2190 2.21 5 O 2649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11970 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1982 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1739 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 749 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "F" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 976 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 874 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 885 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4000 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 21, 'TRANS': 523} Chain breaks: 14 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 113 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.94, per 1000 atoms: 0.83 Number of scatterers: 11970 At special positions: 0 Unit cell: (95.7, 129.525, 181.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 181 15.00 Mg 1 11.99 O 2649 8.00 N 2190 7.00 C 6919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 44.6% alpha, 16.2% beta 75 base pairs and 154 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.623A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'F' and resid 20 through 34 removed outlier: 4.135A pdb=" N SER F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.662A pdb=" N ASP F 47 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 90 Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.030A pdb=" N SER G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.848A pdb=" N LYS G 64 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 92 through 106 removed outlier: 4.546A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 34 removed outlier: 4.165A pdb=" N SER E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.862A pdb=" N ASN H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 87 through 95 removed outlier: 4.072A pdb=" N SER H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 111 removed outlier: 4.026A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 212 removed outlier: 3.697A pdb=" N GLU H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 210 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.592A pdb=" N GLY H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing helix chain 'H' and resid 228 through 232 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 251 through 252 No H-bonds generated for 'chain 'H' and resid 251 through 252' Processing helix chain 'H' and resid 254 through 254 No H-bonds generated for 'chain 'H' and resid 254 through 254' Processing helix chain 'H' and resid 255 through 262 Processing helix chain 'H' and resid 269 through 281 Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.901A pdb=" N ASP H 296 " --> pdb=" O ARG H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 575 through 593 Processing helix chain 'H' and resid 603 through 622 Processing helix chain 'H' and resid 646 through 650 removed outlier: 3.755A pdb=" N MET H 649 " --> pdb=" O LEU H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 798 through 808 Processing helix chain 'H' and resid 822 through 828 removed outlier: 4.025A pdb=" N ALA H 828 " --> pdb=" O GLU H 825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.646A pdb=" N VAL C 44 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA3, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA4, first strand: chain 'G' and resid 13 through 19 Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 6 removed outlier: 5.060A pdb=" N GLN H 155 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AA8, first strand: chain 'H' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB1, first strand: chain 'H' and resid 568 through 572 removed outlier: 6.267A pdb=" N THR H 569 " --> pdb=" O LEU H 814 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER H 816 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE H 571 " --> pdb=" O SER H 816 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA H 790 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 629 through 636 removed outlier: 3.528A pdb=" N SER H 665 " --> pdb=" O ASN H 660 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 756 through 759 removed outlier: 4.190A pdb=" N SER H 739 " --> pdb=" O THR H 746 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 334 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 154 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2705 1.33 - 1.45: 3299 1.45 - 1.57: 6125 1.57 - 1.69: 360 1.69 - 1.81: 57 Bond restraints: 12546 Sorted by residual: bond pdb=" C3' DG A 5 " pdb=" O3' DG A 5 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" C3' DT A 88 " pdb=" C2' DT A 88 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C4' DA A 41 " pdb=" C3' DA A 41 " ideal model delta sigma weight residual 1.523 1.501 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" O4' DT B 32 " pdb=" C1' DT B 32 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C3' DC B 75 " pdb=" C2' DC B 75 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 9.77e-01 ... (remaining 12541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 16627 1.07 - 2.15: 850 2.15 - 3.22: 213 3.22 - 4.29: 17 4.29 - 5.36: 6 Bond angle restraints: 17713 Sorted by residual: angle pdb=" C TYR H 200 " pdb=" N ARG H 201 " pdb=" CA ARG H 201 " ideal model delta sigma weight residual 120.38 124.92 -4.54 1.37e+00 5.33e-01 1.10e+01 angle pdb=" C ASN F 113 " pdb=" N SER F 114 " pdb=" CA SER F 114 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.77e+00 angle pdb=" C3' DG A 5 " pdb=" O3' DG A 5 " pdb=" P DG A 4 " ideal model delta sigma weight residual 120.20 123.90 -3.70 1.50e+00 4.44e-01 6.07e+00 angle pdb=" N ARG H 201 " pdb=" CA ARG H 201 " pdb=" C ARG H 201 " ideal model delta sigma weight residual 111.33 114.14 -2.81 1.21e+00 6.83e-01 5.38e+00 angle pdb=" C3' DT A 44 " pdb=" C2' DT A 44 " pdb=" C1' DT A 44 " ideal model delta sigma weight residual 101.60 98.15 3.45 1.50e+00 4.44e-01 5.28e+00 ... (remaining 17708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 6331 34.33 - 68.66: 834 68.66 - 103.00: 13 103.00 - 137.33: 1 137.33 - 171.66: 1 Dihedral angle restraints: 7180 sinusoidal: 4109 harmonic: 3071 Sorted by residual: dihedral pdb=" CA PHE G 108 " pdb=" C PHE G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU H 26 " pdb=" C LEU H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DG A 5 " pdb=" C3' DG A 5 " pdb=" O3' DG A 5 " pdb=" P DG A 4 " ideal model delta sinusoidal sigma weight residual 220.00 48.34 171.66 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1239 0.027 - 0.053: 507 0.053 - 0.080: 140 0.080 - 0.107: 69 0.107 - 0.133: 27 Chirality restraints: 1982 Sorted by residual: chirality pdb=" CA VAL H 749 " pdb=" N VAL H 749 " pdb=" C VAL H 749 " pdb=" CB VAL H 749 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE D 43 " pdb=" N ILE D 43 " pdb=" C ILE D 43 " pdb=" CB ILE D 43 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE F 116 " pdb=" N ILE F 116 " pdb=" C ILE F 116 " pdb=" CB ILE F 116 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1979 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA A 21 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA A 21 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA A 21 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA A 21 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA A 21 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA A 21 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA A 21 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA A 21 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA A 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA A 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA A 21 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA A 41 " -0.026 2.00e-02 2.50e+03 1.17e-02 3.75e+00 pdb=" N9 DA A 41 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA A 41 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA A 41 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA A 41 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA A 41 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA A 41 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA A 41 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DA A 41 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA A 41 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA A 41 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 60 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO H 61 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " -0.025 5.00e-02 4.00e+02 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 76 2.53 - 3.12: 8600 3.12 - 3.72: 20244 3.72 - 4.31: 27580 4.31 - 4.90: 42299 Nonbonded interactions: 98799 Sorted by model distance: nonbonded pdb=" OP1 DG A -1 " pdb="MG MG H 900 " model vdw 1.940 2.170 nonbonded pdb=" ND1 HIS H 146 " pdb="MG MG H 900 " model vdw 2.020 2.250 nonbonded pdb=" NE2 HIS H 159 " pdb="MG MG H 900 " model vdw 2.046 2.250 nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H 900 " model vdw 2.110 2.250 nonbonded pdb=" OG SER G 89 " pdb=" OE2 GLU G 96 " model vdw 2.133 3.040 ... (remaining 98794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 11 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 75 or (resid 76 through 77 and ( \ name N or name CA or name C or name O or name CB )) or resid 78 through 113)) selection = (chain 'F' and (resid 11 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 59 or resid 63 or (resid 64 and \ (name N or name CA or name C or name O or name CB )) or resid 65 through 75 or ( \ resid 76 through 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 113)) selection = (chain 'G' and (resid 11 through 59 or resid 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 113)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.480 Find NCS groups from input model: 0.240 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 0.046 12546 Z= 0.175 Angle : 0.563 5.364 17713 Z= 0.339 Chirality : 0.036 0.133 1982 Planarity : 0.004 0.044 1654 Dihedral : 22.917 171.661 5186 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.82 % Allowed : 3.87 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1031 helix: 1.06 (0.24), residues: 439 sheet: -0.03 (0.38), residues: 201 loop : -0.71 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 702 HIS 0.006 0.001 HIS H 76 PHE 0.011 0.001 PHE E 4 TYR 0.013 0.001 TYR G 112 ARG 0.003 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.13029 ( 573) hydrogen bonds : angle 6.03602 ( 1474) covalent geometry : bond 0.00374 (12546) covalent geometry : angle 0.56308 (17713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 241 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 THR cc_start: 0.6857 (p) cc_final: 0.6556 (p) REVERT: F 95 ASP cc_start: 0.8513 (m-30) cc_final: 0.8242 (m-30) REVERT: G 93 LYS cc_start: 0.5574 (tttt) cc_final: 0.4296 (mttt) REVERT: G 111 PHE cc_start: 0.6359 (t80) cc_final: 0.6087 (t80) REVERT: H 17 TYR cc_start: 0.7902 (m-80) cc_final: 0.7682 (m-80) REVERT: H 223 MET cc_start: 0.5358 (mmm) cc_final: 0.4533 (mmm) REVERT: H 267 HIS cc_start: 0.5878 (t70) cc_final: 0.5430 (t-90) REVERT: H 621 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7850 (mm110) REVERT: H 815 TYR cc_start: 0.7933 (m-80) cc_final: 0.7434 (m-80) outliers start: 7 outliers final: 1 residues processed: 248 average time/residue: 0.2918 time to fit residues: 96.9928 Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS H 106 HIS H 145 ASN ** H 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.080491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064816 restraints weight = 56697.902| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.67 r_work: 0.3272 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12546 Z= 0.287 Angle : 0.712 13.684 17713 Z= 0.405 Chirality : 0.041 0.157 1982 Planarity : 0.005 0.045 1654 Dihedral : 27.675 168.450 3240 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.35 % Allowed : 13.73 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1031 helix: 0.82 (0.23), residues: 444 sheet: -0.30 (0.35), residues: 211 loop : -0.80 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 638 HIS 0.009 0.002 HIS F 50 PHE 0.023 0.003 PHE E 4 TYR 0.015 0.002 TYR H 291 ARG 0.007 0.001 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.05273 ( 573) hydrogen bonds : angle 4.91033 ( 1474) covalent geometry : bond 0.00644 (12546) covalent geometry : angle 0.71177 (17713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8261 (tp30) cc_final: 0.7981 (tp30) REVERT: F 80 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8198 (mm-40) REVERT: F 108 PHE cc_start: 0.8319 (m-10) cc_final: 0.8119 (m-80) REVERT: G 93 LYS cc_start: 0.5324 (tttt) cc_final: 0.4015 (mttt) REVERT: E 40 GLU cc_start: 0.8170 (tp30) cc_final: 0.7868 (tp30) REVERT: H 223 MET cc_start: 0.4732 (mmm) cc_final: 0.4161 (mmm) REVERT: H 810 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7072 (ptt180) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 0.2991 time to fit residues: 57.8630 Evaluate side-chains 106 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN H 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.080976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.064580 restraints weight = 57522.968| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.96 r_work: 0.3273 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12546 Z= 0.217 Angle : 0.631 13.254 17713 Z= 0.364 Chirality : 0.038 0.200 1982 Planarity : 0.005 0.055 1654 Dihedral : 27.541 166.371 3238 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.46 % Allowed : 14.44 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1031 helix: 0.89 (0.24), residues: 448 sheet: -0.49 (0.34), residues: 216 loop : -0.76 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 277 HIS 0.005 0.001 HIS H 76 PHE 0.018 0.002 PHE F 111 TYR 0.011 0.001 TYR H 200 ARG 0.005 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 573) hydrogen bonds : angle 4.56441 ( 1474) covalent geometry : bond 0.00482 (12546) covalent geometry : angle 0.63053 (17713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8180 (tp30) cc_final: 0.7910 (tp30) REVERT: F 80 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8216 (mm-40) REVERT: G 93 LYS cc_start: 0.5334 (tttt) cc_final: 0.3937 (mttm) REVERT: H 106 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.5711 (t-90) REVERT: H 144 PHE cc_start: 0.7216 (m-80) cc_final: 0.6935 (m-80) REVERT: H 223 MET cc_start: 0.4542 (mmm) cc_final: 0.3953 (mmm) REVERT: H 274 MET cc_start: 0.4929 (ptp) cc_final: 0.4702 (ptp) REVERT: H 566 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.4863 (mtm-85) REVERT: H 810 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7280 (ptt180) outliers start: 21 outliers final: 12 residues processed: 122 average time/residue: 0.2640 time to fit residues: 48.4801 Evaluate side-chains 106 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.080673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.062294 restraints weight = 56618.217| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.73 r_work: 0.3292 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12546 Z= 0.211 Angle : 0.622 12.553 17713 Z= 0.358 Chirality : 0.038 0.217 1982 Planarity : 0.004 0.055 1654 Dihedral : 27.505 161.865 3238 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.52 % Allowed : 13.15 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1031 helix: 0.77 (0.24), residues: 456 sheet: -0.56 (0.33), residues: 223 loop : -0.84 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 277 HIS 0.004 0.001 HIS H 76 PHE 0.030 0.002 PHE F 111 TYR 0.010 0.001 TYR H 200 ARG 0.004 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 573) hydrogen bonds : angle 4.41291 ( 1474) covalent geometry : bond 0.00472 (12546) covalent geometry : angle 0.62183 (17713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 80 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8170 (mm-40) REVERT: F 111 PHE cc_start: 0.6223 (t80) cc_final: 0.5817 (t80) REVERT: G 37 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7807 (mmt180) REVERT: G 81 LEU cc_start: 0.3831 (OUTLIER) cc_final: 0.3606 (mm) REVERT: G 93 LYS cc_start: 0.5214 (tttt) cc_final: 0.3829 (mttm) REVERT: G 111 PHE cc_start: 0.6806 (t80) cc_final: 0.6482 (t80) REVERT: H 106 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.5568 (t-90) REVERT: H 144 PHE cc_start: 0.7313 (m-80) cc_final: 0.7081 (m-80) REVERT: H 223 MET cc_start: 0.4183 (mmm) cc_final: 0.3429 (mmm) REVERT: H 566 ARG cc_start: 0.5918 (OUTLIER) cc_final: 0.4943 (mtm-85) REVERT: H 810 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6729 (ptt180) outliers start: 30 outliers final: 19 residues processed: 128 average time/residue: 0.2222 time to fit residues: 42.6300 Evaluate side-chains 114 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.081451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.063212 restraints weight = 57067.290| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.76 r_work: 0.3322 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12546 Z= 0.162 Angle : 0.590 11.670 17713 Z= 0.340 Chirality : 0.036 0.200 1982 Planarity : 0.004 0.053 1654 Dihedral : 27.357 159.095 3238 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 13.73 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1031 helix: 0.95 (0.24), residues: 455 sheet: -0.47 (0.33), residues: 225 loop : -0.82 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 774 HIS 0.009 0.001 HIS G 50 PHE 0.022 0.002 PHE F 111 TYR 0.010 0.001 TYR H 200 ARG 0.003 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 573) hydrogen bonds : angle 4.26121 ( 1474) covalent geometry : bond 0.00353 (12546) covalent geometry : angle 0.59045 (17713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 52 TYR cc_start: 0.4444 (m-80) cc_final: 0.4107 (m-80) REVERT: G 93 LYS cc_start: 0.5156 (tttt) cc_final: 0.3965 (mttm) REVERT: H 106 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.5717 (t-90) REVERT: H 223 MET cc_start: 0.4008 (mmm) cc_final: 0.2863 (mmt) REVERT: H 566 ARG cc_start: 0.5835 (OUTLIER) cc_final: 0.4907 (mtm-85) REVERT: H 810 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6513 (ptt180) outliers start: 26 outliers final: 19 residues processed: 127 average time/residue: 0.2245 time to fit residues: 42.4872 Evaluate side-chains 113 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 HIS H 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.082314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064157 restraints weight = 57981.589| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.83 r_work: 0.3348 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12546 Z= 0.141 Angle : 0.582 10.600 17713 Z= 0.331 Chirality : 0.035 0.159 1982 Planarity : 0.004 0.053 1654 Dihedral : 27.185 155.054 3238 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.17 % Allowed : 14.55 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1031 helix: 1.06 (0.24), residues: 454 sheet: -0.51 (0.34), residues: 225 loop : -0.72 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 638 HIS 0.004 0.001 HIS H 157 PHE 0.023 0.001 PHE F 111 TYR 0.009 0.001 TYR H 200 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 573) hydrogen bonds : angle 4.14004 ( 1474) covalent geometry : bond 0.00304 (12546) covalent geometry : angle 0.58151 (17713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7534 (mmt-90) REVERT: G 52 TYR cc_start: 0.4621 (m-80) cc_final: 0.4333 (m-80) REVERT: G 81 LEU cc_start: 0.3659 (OUTLIER) cc_final: 0.3394 (mm) REVERT: G 93 LYS cc_start: 0.5152 (tttt) cc_final: 0.3997 (mttm) REVERT: G 111 PHE cc_start: 0.6785 (t80) cc_final: 0.6224 (t80) REVERT: H 106 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.6313 (t70) REVERT: H 223 MET cc_start: 0.3859 (mmm) cc_final: 0.3278 (mmt) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.2102 time to fit residues: 42.8225 Evaluate side-chains 113 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.079587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.063444 restraints weight = 58053.431| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.89 r_work: 0.3256 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12546 Z= 0.270 Angle : 0.674 9.913 17713 Z= 0.381 Chirality : 0.040 0.312 1982 Planarity : 0.005 0.048 1654 Dihedral : 27.501 147.328 3238 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.64 % Allowed : 16.08 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1031 helix: 0.77 (0.24), residues: 456 sheet: -0.57 (0.34), residues: 226 loop : -0.83 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 638 HIS 0.013 0.002 HIS F 104 PHE 0.021 0.002 PHE D 51 TYR 0.013 0.002 TYR G 112 ARG 0.010 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 573) hydrogen bonds : angle 4.52830 ( 1474) covalent geometry : bond 0.00607 (12546) covalent geometry : angle 0.67397 (17713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 81 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3507 (mm) REVERT: G 93 LYS cc_start: 0.5154 (tttt) cc_final: 0.3693 (mttm) REVERT: H 106 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.5716 (t-90) REVERT: H 566 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5216 (mtm-85) REVERT: H 810 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7286 (ptt180) outliers start: 31 outliers final: 22 residues processed: 120 average time/residue: 0.2133 time to fit residues: 38.3891 Evaluate side-chains 115 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN H 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.081271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.064343 restraints weight = 57726.632| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.77 r_work: 0.3298 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12546 Z= 0.158 Angle : 0.601 10.008 17713 Z= 0.340 Chirality : 0.035 0.162 1982 Planarity : 0.004 0.058 1654 Dihedral : 27.196 148.838 3238 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.40 % Allowed : 17.25 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 1031 helix: 1.15 (0.24), residues: 453 sheet: -0.70 (0.33), residues: 230 loop : -0.77 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 638 HIS 0.005 0.001 HIS F 104 PHE 0.014 0.001 PHE H 144 TYR 0.009 0.001 TYR H 200 ARG 0.005 0.000 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 573) hydrogen bonds : angle 4.22416 ( 1474) covalent geometry : bond 0.00346 (12546) covalent geometry : angle 0.60128 (17713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 52 TYR cc_start: 0.4543 (m-80) cc_final: 0.4175 (m-80) REVERT: G 81 LEU cc_start: 0.3465 (OUTLIER) cc_final: 0.3225 (mm) REVERT: G 93 LYS cc_start: 0.5183 (tttt) cc_final: 0.3863 (mttm) REVERT: H 106 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.5609 (t-90) REVERT: H 566 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5167 (mtm-85) outliers start: 29 outliers final: 23 residues processed: 129 average time/residue: 0.2115 time to fit residues: 40.9807 Evaluate side-chains 119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 679 HIS Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.079542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063511 restraints weight = 58316.268| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.88 r_work: 0.3251 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12546 Z= 0.266 Angle : 0.681 11.093 17713 Z= 0.381 Chirality : 0.040 0.187 1982 Planarity : 0.005 0.056 1654 Dihedral : 27.454 145.427 3238 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.29 % Allowed : 17.72 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1031 helix: 0.82 (0.24), residues: 455 sheet: -0.71 (0.34), residues: 224 loop : -0.79 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 638 HIS 0.011 0.002 HIS F 104 PHE 0.021 0.002 PHE D 51 TYR 0.009 0.001 TYR G 52 ARG 0.007 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 573) hydrogen bonds : angle 4.49134 ( 1474) covalent geometry : bond 0.00601 (12546) covalent geometry : angle 0.68065 (17713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 81 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3364 (mm) REVERT: G 93 LYS cc_start: 0.5066 (tttt) cc_final: 0.3777 (mttm) REVERT: H 106 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5564 (t-90) REVERT: H 274 MET cc_start: 0.6953 (ppp) cc_final: 0.6177 (ptp) REVERT: H 566 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5071 (mtm-85) REVERT: H 810 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6494 (ptt180) outliers start: 28 outliers final: 24 residues processed: 118 average time/residue: 0.2223 time to fit residues: 39.2225 Evaluate side-chains 120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.080442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064469 restraints weight = 57842.192| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.81 r_work: 0.3284 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12546 Z= 0.195 Angle : 0.641 11.397 17713 Z= 0.361 Chirality : 0.038 0.314 1982 Planarity : 0.004 0.056 1654 Dihedral : 27.321 147.689 3238 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.05 % Allowed : 18.31 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1031 helix: 0.93 (0.24), residues: 454 sheet: -0.73 (0.34), residues: 229 loop : -0.76 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 638 HIS 0.006 0.001 HIS F 104 PHE 0.013 0.002 PHE D 51 TYR 0.009 0.001 TYR H 200 ARG 0.006 0.000 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 573) hydrogen bonds : angle 4.36447 ( 1474) covalent geometry : bond 0.00437 (12546) covalent geometry : angle 0.64106 (17713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 52 TYR cc_start: 0.4537 (m-80) cc_final: 0.4072 (m-80) REVERT: G 81 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.3222 (mm) REVERT: G 93 LYS cc_start: 0.5166 (tttt) cc_final: 0.3838 (mttm) REVERT: H 106 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5431 (t-90) REVERT: H 274 MET cc_start: 0.6791 (ppp) cc_final: 0.6044 (ptp) REVERT: H 566 ARG cc_start: 0.5719 (OUTLIER) cc_final: 0.5103 (mtm-85) outliers start: 26 outliers final: 22 residues processed: 115 average time/residue: 0.2150 time to fit residues: 36.8905 Evaluate side-chains 116 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 HIS H 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.081713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.063648 restraints weight = 57826.845| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.77 r_work: 0.3338 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12546 Z= 0.153 Angle : 0.608 11.022 17713 Z= 0.342 Chirality : 0.035 0.206 1982 Planarity : 0.004 0.056 1654 Dihedral : 27.063 147.807 3238 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.93 % Allowed : 18.19 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 1031 helix: 1.25 (0.24), residues: 445 sheet: -0.70 (0.33), residues: 232 loop : -0.79 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 638 HIS 0.007 0.001 HIS G 48 PHE 0.012 0.001 PHE F 111 TYR 0.009 0.001 TYR H 200 ARG 0.004 0.000 ARG G 51 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 573) hydrogen bonds : angle 4.15431 ( 1474) covalent geometry : bond 0.00336 (12546) covalent geometry : angle 0.60819 (17713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8548.18 seconds wall clock time: 153 minutes 13.49 seconds (9193.49 seconds total)