Starting phenix.real_space_refine on Wed Sep 17 22:24:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0z_50119/09_2025/9f0z_50119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0z_50119/09_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_50119/09_2025/9f0z_50119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0z_50119/09_2025/9f0z_50119.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0z_50119/09_2025/9f0z_50119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0z_50119/09_2025/9f0z_50119.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2} 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: {'TRP:plan': 1, 'GLN:plan1': 6, 'ARG:plan': 4, 'GLU:plan': 9, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} 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: 3.06, per 1000 atoms: 0.26 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: 1.05 Conformation dependent library (CDL) restraints added in 437.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.55 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: 2.65 Time building geometry restraints manager: 1.42 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: 16.170 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.040 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.000 ------------------------------------------------------------------------------- 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 : 7.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E 32 TYR 0.013 0.001 TYR G 112 PHE 0.011 0.001 PHE E 4 TRP 0.004 0.001 TRP H 702 HIS 0.006 0.001 HIS H 76 Details of bonding type rmsd covalent geometry : bond 0.00374 (12546) covalent geometry : angle 0.56308 (17713) hydrogen bonds : bond 0.13029 ( 573) hydrogen bonds : angle 6.03602 ( 1474) *********************** 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 : 0.367 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: 0.1435 time to fit residues: 47.6685 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 : 0.431 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.079684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063537 restraints weight = 57102.788| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.97 r_work: 0.3241 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 12546 Z= 0.348 Angle : 0.755 12.701 17713 Z= 0.429 Chirality : 0.044 0.219 1982 Planarity : 0.006 0.051 1654 Dihedral : 27.822 167.712 3240 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.58 % Allowed : 13.97 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.25), residues: 1031 helix: 0.58 (0.23), residues: 446 sheet: -0.35 (0.35), residues: 211 loop : -0.89 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 88 TYR 0.017 0.002 TYR H 213 PHE 0.027 0.003 PHE G 108 TRP 0.010 0.002 TRP H 172 HIS 0.008 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00787 (12546) covalent geometry : angle 0.75521 (17713) hydrogen bonds : bond 0.05875 ( 573) hydrogen bonds : angle 5.09369 ( 1474) *********************** 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 128 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 80 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8203 (mm-40) REVERT: F 108 PHE cc_start: 0.8356 (m-10) cc_final: 0.8079 (m-80) REVERT: G 45 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7112 (mt) REVERT: G 93 LYS cc_start: 0.5303 (tttt) cc_final: 0.4050 (mttt) REVERT: E 40 GLU cc_start: 0.8306 (tp30) cc_final: 0.8019 (tp30) REVERT: E 72 MET cc_start: 0.8471 (mtp) cc_final: 0.8266 (ttm) REVERT: H 223 MET cc_start: 0.4580 (mmm) cc_final: 0.3933 (mmm) REVERT: H 810 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7083 (ptt180) outliers start: 22 outliers final: 12 residues processed: 127 average time/residue: 0.1006 time to fit residues: 19.1667 Evaluate side-chains 104 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 24 SER 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 107 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.081166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.064688 restraints weight = 56775.536| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.82 r_work: 0.3288 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12546 Z= 0.186 Angle : 0.614 12.090 17713 Z= 0.356 Chirality : 0.037 0.193 1982 Planarity : 0.004 0.054 1654 Dihedral : 27.556 165.905 3238 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.82 % Allowed : 13.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.26), residues: 1031 helix: 0.84 (0.24), residues: 449 sheet: -0.38 (0.34), residues: 214 loop : -0.81 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 88 TYR 0.009 0.001 TYR H 200 PHE 0.018 0.002 PHE F 111 TRP 0.013 0.001 TRP H 277 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00409 (12546) covalent geometry : angle 0.61413 (17713) hydrogen bonds : bond 0.04003 ( 573) hydrogen bonds : angle 4.54407 ( 1474) *********************** 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 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8614 (tp30) cc_final: 0.8147 (tp30) REVERT: F 80 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8229 (mm-40) REVERT: G 93 LYS cc_start: 0.5332 (tttt) cc_final: 0.3907 (mttm) REVERT: E 40 GLU cc_start: 0.8099 (tp30) cc_final: 0.7868 (tp30) REVERT: H 106 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5753 (t-90) REVERT: H 223 MET cc_start: 0.4458 (mmm) cc_final: 0.3752 (mmm) REVERT: H 566 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.4754 (mtm-85) REVERT: H 810 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7285 (ptt180) outliers start: 24 outliers final: 11 residues processed: 128 average time/residue: 0.1074 time to fit residues: 20.2764 Evaluate side-chains 106 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 12 LYS 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 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 810 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.081778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063442 restraints weight = 57252.460| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.80 r_work: 0.3324 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3331 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= 0.159 Angle : 0.585 11.566 17713 Z= 0.339 Chirality : 0.036 0.151 1982 Planarity : 0.004 0.049 1654 Dihedral : 27.373 163.925 3238 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.93 % Allowed : 13.26 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1031 helix: 1.00 (0.24), residues: 449 sheet: -0.53 (0.34), residues: 223 loop : -0.61 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.010 0.001 TYR H 200 PHE 0.031 0.002 PHE F 111 TRP 0.010 0.001 TRP H 277 HIS 0.003 0.001 HIS H 76 Details of bonding type rmsd covalent geometry : bond 0.00347 (12546) covalent geometry : angle 0.58484 (17713) hydrogen bonds : bond 0.03563 ( 573) hydrogen bonds : angle 4.30440 ( 1474) *********************** 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 131 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8580 (tp30) cc_final: 0.8082 (tp30) REVERT: F 80 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8170 (mm-40) REVERT: G 37 ARG cc_start: 0.7950 (mmt180) cc_final: 0.7571 (mmt-90) REVERT: G 52 TYR cc_start: 0.4381 (m-80) cc_final: 0.3979 (m-80) REVERT: G 81 LEU cc_start: 0.3642 (OUTLIER) cc_final: 0.3417 (mm) REVERT: G 93 LYS cc_start: 0.5270 (tttt) cc_final: 0.4037 (mttm) REVERT: G 111 PHE cc_start: 0.6727 (t80) cc_final: 0.5647 (t80) REVERT: E 40 GLU cc_start: 0.8009 (tp30) cc_final: 0.7735 (tp30) REVERT: H 106 HIS cc_start: 0.6520 (OUTLIER) cc_final: 0.5506 (t-90) REVERT: H 144 PHE cc_start: 0.7043 (m-80) cc_final: 0.6817 (m-80) REVERT: H 223 MET cc_start: 0.4106 (mmm) cc_final: 0.3313 (mmm) REVERT: H 566 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.4845 (mtm-85) REVERT: H 810 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6577 (ptt180) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 0.1062 time to fit residues: 20.1701 Evaluate side-chains 112 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR 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 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET 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 810 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.081381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063133 restraints weight = 57648.108| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.82 r_work: 0.3318 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12546 Z= 0.171 Angle : 0.591 10.855 17713 Z= 0.340 Chirality : 0.036 0.155 1982 Planarity : 0.004 0.045 1654 Dihedral : 27.351 160.201 3238 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.17 % Allowed : 13.03 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1031 helix: 1.03 (0.24), residues: 454 sheet: -0.45 (0.34), residues: 223 loop : -0.74 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 57 TYR 0.012 0.001 TYR H 200 PHE 0.024 0.002 PHE F 111 TRP 0.017 0.001 TRP H 638 HIS 0.003 0.001 HIS H 76 Details of bonding type rmsd covalent geometry : bond 0.00377 (12546) covalent geometry : angle 0.59090 (17713) hydrogen bonds : bond 0.03709 ( 573) hydrogen bonds : angle 4.27590 ( 1474) *********************** 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 131 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8569 (tp30) cc_final: 0.8115 (tp30) REVERT: F 80 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8192 (mm-40) REVERT: G 37 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7845 (mmt-90) REVERT: G 50 HIS cc_start: 0.8023 (m170) cc_final: 0.7788 (m90) REVERT: G 81 LEU cc_start: 0.3730 (OUTLIER) cc_final: 0.3490 (mm) REVERT: G 93 LYS cc_start: 0.5184 (tttt) cc_final: 0.3986 (mttm) REVERT: G 108 PHE cc_start: 0.6795 (m-80) cc_final: 0.6460 (m-80) REVERT: G 109 PRO cc_start: 0.2808 (Cg_exo) cc_final: 0.2385 (Cg_endo) REVERT: E 40 GLU cc_start: 0.8064 (tp30) cc_final: 0.7811 (tp30) REVERT: H 106 HIS cc_start: 0.6568 (OUTLIER) cc_final: 0.5540 (t-90) REVERT: H 223 MET cc_start: 0.3970 (mmm) cc_final: 0.2981 (mmt) REVERT: H 810 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6466 (ptt180) outliers start: 27 outliers final: 16 residues processed: 127 average time/residue: 0.1019 time to fit residues: 19.7183 Evaluate side-chains 112 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 106 HIS Chi-restraints excluded: chain H residue 166 THR 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 810 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 56 optimal weight: 0.0050 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.081762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.063589 restraints weight = 57855.767| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.78 r_work: 0.3331 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12546 Z= 0.158 Angle : 0.595 10.932 17713 Z= 0.337 Chirality : 0.036 0.286 1982 Planarity : 0.004 0.044 1654 Dihedral : 27.258 156.738 3238 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.17 % Allowed : 14.67 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.27), residues: 1031 helix: 1.05 (0.24), residues: 454 sheet: -0.43 (0.33), residues: 231 loop : -0.74 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 118 TYR 0.011 0.001 TYR H 200 PHE 0.013 0.001 PHE F 108 TRP 0.024 0.002 TRP H 638 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00346 (12546) covalent geometry : angle 0.59452 (17713) hydrogen bonds : bond 0.03485 ( 573) hydrogen bonds : angle 4.14458 ( 1474) *********************** 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 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8544 (tm-30) REVERT: F 40 GLU cc_start: 0.8541 (tp30) cc_final: 0.8112 (tp30) REVERT: F 80 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8207 (mm-40) REVERT: G 13 MET cc_start: 0.7145 (tpt) cc_final: 0.6938 (tpt) REVERT: G 37 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7881 (mmt-90) REVERT: G 50 HIS cc_start: 0.8066 (m170) cc_final: 0.7788 (m90) REVERT: G 52 TYR cc_start: 0.4329 (m-80) cc_final: 0.3985 (m-80) REVERT: G 93 LYS cc_start: 0.5076 (tttt) cc_final: 0.3921 (mttm) REVERT: E 40 GLU cc_start: 0.8026 (tp30) cc_final: 0.7766 (tp30) REVERT: H 106 HIS cc_start: 0.6468 (OUTLIER) cc_final: 0.5571 (t-90) REVERT: H 223 MET cc_start: 0.3849 (mmm) cc_final: 0.3214 (mmt) REVERT: H 566 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.4967 (mtm-85) REVERT: H 810 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6379 (ptt180) outliers start: 27 outliers final: 18 residues processed: 132 average time/residue: 0.1100 time to fit residues: 21.5036 Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 G residue 18 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.080656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.064570 restraints weight = 57744.143| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.82 r_work: 0.3279 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12546 Z= 0.206 Angle : 0.624 11.130 17713 Z= 0.354 Chirality : 0.037 0.216 1982 Planarity : 0.004 0.044 1654 Dihedral : 27.311 150.889 3238 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.40 % Allowed : 14.91 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.27), residues: 1031 helix: 0.89 (0.24), residues: 457 sheet: -0.56 (0.33), residues: 232 loop : -0.69 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 734 TYR 0.009 0.001 TYR H 200 PHE 0.025 0.002 PHE F 111 TRP 0.021 0.002 TRP H 638 HIS 0.011 0.001 HIS H 146 Details of bonding type rmsd covalent geometry : bond 0.00462 (12546) covalent geometry : angle 0.62441 (17713) hydrogen bonds : bond 0.04032 ( 573) hydrogen bonds : angle 4.28838 ( 1474) *********************** 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 127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8524 (tp30) cc_final: 0.8149 (tp30) REVERT: G 50 HIS cc_start: 0.8021 (m170) cc_final: 0.7720 (m90) REVERT: G 81 LEU cc_start: 0.3777 (OUTLIER) cc_final: 0.3533 (mm) REVERT: G 93 LYS cc_start: 0.5032 (tttt) cc_final: 0.3905 (mttm) REVERT: G 111 PHE cc_start: 0.6543 (t80) cc_final: 0.6229 (t80) REVERT: E 40 GLU cc_start: 0.8117 (tp30) cc_final: 0.7892 (tp30) REVERT: H 106 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.5518 (t-90) REVERT: H 566 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.5196 (mtm-85) REVERT: H 810 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7187 (ptt180) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.0996 time to fit residues: 18.9918 Evaluate side-chains 124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 22 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.081455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.063305 restraints weight = 57254.446| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.75 r_work: 0.3328 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12546 Z= 0.161 Angle : 0.609 11.546 17713 Z= 0.343 Chirality : 0.036 0.259 1982 Planarity : 0.004 0.056 1654 Dihedral : 27.166 148.281 3238 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.17 % Allowed : 15.85 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.27), residues: 1031 helix: 0.97 (0.24), residues: 457 sheet: -0.64 (0.33), residues: 232 loop : -0.65 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 118 TYR 0.008 0.001 TYR H 200 PHE 0.025 0.002 PHE F 111 TRP 0.021 0.002 TRP H 638 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00357 (12546) covalent geometry : angle 0.60890 (17713) hydrogen bonds : bond 0.03478 ( 573) hydrogen bonds : angle 4.23922 ( 1474) *********************** 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 131 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 40 GLU cc_start: 0.8497 (tp30) cc_final: 0.8115 (tp30) REVERT: F 80 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8278 (mm-40) REVERT: G 50 HIS cc_start: 0.8039 (m170) cc_final: 0.7754 (m90) REVERT: G 81 LEU cc_start: 0.3764 (OUTLIER) cc_final: 0.3520 (mm) REVERT: G 93 LYS cc_start: 0.5193 (tttt) cc_final: 0.3958 (mttm) REVERT: G 111 PHE cc_start: 0.6374 (t80) cc_final: 0.6071 (t80) REVERT: E 40 GLU cc_start: 0.8004 (tp30) cc_final: 0.7752 (tp30) REVERT: H 106 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.5488 (t-90) REVERT: H 566 ARG cc_start: 0.5721 (OUTLIER) cc_final: 0.5072 (mtm-85) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 0.0971 time to fit residues: 19.1403 Evaluate side-chains 123 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 VAL 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 692 VAL Chi-restraints excluded: chain H residue 700 SER 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 85 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.080879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062675 restraints weight = 56965.589| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.75 r_work: 0.3310 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12546 Z= 0.198 Angle : 0.638 13.535 17713 Z= 0.357 Chirality : 0.037 0.249 1982 Planarity : 0.004 0.043 1654 Dihedral : 27.191 147.656 3238 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.52 % Allowed : 16.43 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.27), residues: 1031 helix: 0.87 (0.24), residues: 457 sheet: -0.71 (0.33), residues: 230 loop : -0.67 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 237 TYR 0.010 0.001 TYR G 112 PHE 0.015 0.002 PHE F 111 TRP 0.017 0.001 TRP H 638 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00444 (12546) covalent geometry : angle 0.63795 (17713) hydrogen bonds : bond 0.03940 ( 573) hydrogen bonds : angle 4.29991 ( 1474) *********************** 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 129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8569 (tm-30) REVERT: F 40 GLU cc_start: 0.8492 (tp30) cc_final: 0.8131 (tp30) REVERT: F 80 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8268 (mm-40) REVERT: G 37 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7585 (mmt-90) REVERT: G 50 HIS cc_start: 0.8055 (m170) cc_final: 0.7764 (m90) REVERT: G 81 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3528 (mm) REVERT: G 93 LYS cc_start: 0.5177 (tttt) cc_final: 0.3887 (mttm) REVERT: G 111 PHE cc_start: 0.6476 (t80) cc_final: 0.6206 (t80) REVERT: E 40 GLU cc_start: 0.8017 (tp30) cc_final: 0.7769 (tp30) REVERT: H 2 MET cc_start: 0.6175 (mpp) cc_final: 0.5376 (mmp) REVERT: H 106 HIS cc_start: 0.6394 (OUTLIER) cc_final: 0.5428 (t-90) REVERT: H 566 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.5090 (mtm-85) REVERT: H 810 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7254 (ptt180) outliers start: 30 outliers final: 23 residues processed: 125 average time/residue: 0.0950 time to fit residues: 18.2087 Evaluate side-chains 124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 87 ASN 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 22 VAL 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 692 VAL Chi-restraints excluded: chain H residue 700 SER 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 23 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.081432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.065132 restraints weight = 57563.511| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.85 r_work: 0.3307 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12546 Z= 0.168 Angle : 0.622 13.550 17713 Z= 0.346 Chirality : 0.036 0.192 1982 Planarity : 0.004 0.058 1654 Dihedral : 27.111 146.104 3238 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.17 % Allowed : 16.67 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.27), residues: 1031 helix: 0.95 (0.24), residues: 457 sheet: -0.68 (0.33), residues: 230 loop : -0.65 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 118 TYR 0.008 0.001 TYR H 200 PHE 0.018 0.001 PHE F 111 TRP 0.021 0.001 TRP H 638 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00373 (12546) covalent geometry : angle 0.62198 (17713) hydrogen bonds : bond 0.03625 ( 573) hydrogen bonds : angle 4.24571 ( 1474) ********************** 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 128 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 40 GLU cc_start: 0.8480 (tp30) cc_final: 0.8145 (tp30) REVERT: F 80 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8282 (mm-40) REVERT: G 37 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7524 (mmt-90) REVERT: G 50 HIS cc_start: 0.8023 (m170) cc_final: 0.7702 (m90) REVERT: G 81 LEU cc_start: 0.3611 (OUTLIER) cc_final: 0.3346 (mm) REVERT: G 93 LYS cc_start: 0.5192 (tttt) cc_final: 0.3844 (mttm) REVERT: E 40 GLU cc_start: 0.8039 (tp30) cc_final: 0.7791 (tp30) REVERT: H 1 MET cc_start: 0.0012 (tpp) cc_final: -0.0335 (tpt) REVERT: H 2 MET cc_start: 0.6102 (mpp) cc_final: 0.5801 (mmp) REVERT: H 106 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.5532 (t-90) REVERT: H 141 MET cc_start: 0.8022 (ppp) cc_final: 0.7272 (tmm) REVERT: H 223 MET cc_start: 0.3308 (mmm) cc_final: 0.2551 (mmt) REVERT: H 566 ARG cc_start: 0.5632 (OUTLIER) cc_final: 0.5056 (mtm-85) REVERT: H 810 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7073 (ptt180) outliers start: 27 outliers final: 22 residues processed: 126 average time/residue: 0.0935 time to fit residues: 18.0164 Evaluate side-chains 124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 22 VAL 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 692 VAL Chi-restraints excluded: chain H residue 700 SER 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 19 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 0.0370 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 79 optimal weight: 9.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.082355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065264 restraints weight = 57687.056| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.67 r_work: 0.3321 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4376 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= 0.147 Angle : 0.612 13.422 17713 Z= 0.340 Chirality : 0.035 0.168 1982 Planarity : 0.004 0.043 1654 Dihedral : 26.981 144.672 3238 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 17.14 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.27), residues: 1031 helix: 1.20 (0.25), residues: 450 sheet: -0.62 (0.35), residues: 216 loop : -0.63 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 237 TYR 0.008 0.001 TYR G 112 PHE 0.014 0.001 PHE F 111 TRP 0.009 0.001 TRP H 277 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00322 (12546) covalent geometry : angle 0.61231 (17713) hydrogen bonds : bond 0.03426 ( 573) hydrogen bonds : angle 4.13394 ( 1474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.22 seconds wall clock time: 63 minutes 19.78 seconds (3799.78 seconds total)