Starting phenix.real_space_refine on Wed Mar 4 13:50:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6px3_20517/03_2026/6px3_20517.cif Found real_map, /net/cci-nas-00/data/ceres_data/6px3_20517/03_2026/6px3_20517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6px3_20517/03_2026/6px3_20517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6px3_20517/03_2026/6px3_20517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6px3_20517/03_2026/6px3_20517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6px3_20517/03_2026/6px3_20517.map" } resolution = 4.1 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= 0.004 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 Zn 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 8074 2.51 5 N 2663 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14323 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1393 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1816 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12981 SG CYS S 158 59.132 83.833 47.890 1.00358.91 S ATOM 13014 SG CYS S 163 61.737 82.243 50.744 1.00359.20 S ATOM 13051 SG CYS S 169 61.811 82.426 46.323 1.00377.57 S ATOM 12758 SG CYS S 129 58.755 80.167 51.153 1.00321.15 S ATOM 12772 SG CYS S 131 58.781 77.155 49.607 1.00322.61 S ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12910 SG CYS S 149 58.173 78.238 47.291 1.00299.48 S ATOM 13819 SG CYS S 261 37.845 88.685 19.012 1.00396.58 S ATOM 14198 SG CYS S 308 40.086 91.078 16.518 1.00413.35 S ATOM 14216 SG CYS S 310 40.442 89.010 15.411 1.00394.48 S ATOM 14250 SG CYS S 315 37.517 90.048 15.112 1.00394.57 S Time building chain proxies: 3.38, per 1000 atoms: 0.24 Number of scatterers: 14323 At special positions: 0 Unit cell: (93.6, 145.6, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 290 15.00 O 3260 8.00 N 2663 7.00 C 8074 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: 1.13 Conformation dependent library (CDL) restraints added in 532.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 56.8% alpha, 7.1% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid -50 through -37 Processing helix chain 'C' and resid -35 through -33 No H-bonds generated for 'chain 'C' and resid -35 through -33' Processing helix chain 'C' and resid -17 through -12 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.632A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.547A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.600A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.827A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid -60 through -56 removed outlier: 8.790A pdb=" N LEU C -5 " --> pdb=" O GLN C -70 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C -68 " --> pdb=" O LEU C -5 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU C -3 " --> pdb=" O PHE C -68 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C -66 " --> pdb=" O LEU C -3 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU C -1 " --> pdb=" O LYS C -66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB5, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.714A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 212 through 214 466 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 1.63 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: 2342 1.33 - 1.45: 5126 1.45 - 1.57: 7067 1.57 - 1.69: 578 1.69 - 1.81: 48 Bond restraints: 15161 Sorted by residual: bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.29e+01 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.392 -0.058 1.51e-02 4.39e+03 1.47e+01 bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.422 1.501 -0.079 3.00e-02 1.11e+03 6.86e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.95e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20704 2.05 - 4.09: 922 4.09 - 6.14: 59 6.14 - 8.18: 14 8.18 - 10.23: 3 Bond angle restraints: 21702 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.41 -7.03 1.05e+00 9.07e-01 4.48e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.25 -7.25 1.10e+00 8.26e-01 4.34e+01 angle pdb=" C SER S 122 " pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 122.61 129.80 -7.19 1.56e+00 4.11e-01 2.12e+01 angle pdb=" N VAL S 159 " pdb=" CA VAL S 159 " pdb=" C VAL S 159 " ideal model delta sigma weight residual 110.05 105.58 4.47 1.09e+00 8.42e-01 1.68e+01 ... (remaining 21697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 6839 34.59 - 69.19: 1517 69.19 - 103.78: 17 103.78 - 138.38: 0 138.38 - 172.97: 4 Dihedral angle restraints: 8377 sinusoidal: 5318 harmonic: 3059 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.03 172.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1769 0.057 - 0.113: 550 0.113 - 0.170: 98 0.170 - 0.227: 25 0.227 - 0.283: 5 Chirality restraints: 2447 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO S 88 " pdb=" N PRO S 88 " pdb=" C PRO S 88 " pdb=" CB PRO S 88 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2444 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.60e-02 7.71e+00 pdb=" N9 DG J 106 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 2 1.67 - 2.48: 35 2.48 - 3.28: 14016 3.28 - 4.09: 41685 4.09 - 4.90: 65863 Warning: very small nonbonded interaction distances. Nonbonded interactions: 121601 Sorted by model distance: nonbonded pdb=" O GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 0.861 3.040 nonbonded pdb=" O GLN C -23 " pdb=" CD GLU D 102 " model vdw 1.590 3.270 nonbonded pdb=" O GLY C -25 " pdb=" OD1 ASP C 90 " model vdw 1.742 3.040 nonbonded pdb=" C GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 1.788 3.270 nonbonded pdb=" NE2 GLN C -23 " pdb=" CE1 HIS D 106 " model vdw 2.014 3.340 ... (remaining 121596 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 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'D' and resid 27 through 120) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.89 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 19.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.008 0.165 15173 Z= 0.363 Angle : 1.211 47.524 21720 Z= 0.590 Chirality : 0.057 0.283 2447 Planarity : 0.007 0.056 1760 Dihedral : 26.725 172.971 6407 Min Nonbonded Distance : 0.861 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 0.45 % Allowed : 5.76 % Favored : 93.79 % 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 are not related in a simple way. whole: -0.93 (0.23), residues: 1033 helix: 0.14 (0.19), residues: 564 sheet: -1.34 (0.57), residues: 71 loop : -1.49 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.017 0.003 TYR H 118 PHE 0.024 0.003 PHE B 61 TRP 0.005 0.002 TRP S 135 HIS 0.005 0.001 HIS C -4 Details of bonding type rmsd covalent geometry : bond 0.00754 (15161) covalent geometry : angle 0.94118 (21702) hydrogen bonds : bond 0.11466 ( 834) hydrogen bonds : angle 4.30700 ( 2077) metal coordination : bond 0.07879 ( 12) metal coordination : angle 26.50171 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 381 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9681 (m) cc_final: 0.9394 (p) REVERT: A 68 GLN cc_start: 0.9771 (tt0) cc_final: 0.9237 (tp-100) REVERT: A 80 THR cc_start: 0.9356 (m) cc_final: 0.8912 (p) REVERT: A 81 ASP cc_start: 0.8742 (t0) cc_final: 0.8414 (t0) REVERT: A 94 GLU cc_start: 0.8893 (tp30) cc_final: 0.8002 (tm-30) REVERT: A 105 GLU cc_start: 0.9274 (tp30) cc_final: 0.8923 (tm-30) REVERT: B 44 LYS cc_start: 0.9444 (tttt) cc_final: 0.9184 (ttpt) REVERT: B 49 LEU cc_start: 0.9752 (mt) cc_final: 0.9216 (mm) REVERT: B 59 LYS cc_start: 0.9615 (ttpt) cc_final: 0.9218 (tppp) REVERT: B 70 VAL cc_start: 0.9699 (t) cc_final: 0.9339 (p) REVERT: B 74 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8726 (pt0) REVERT: B 81 VAL cc_start: 0.9671 (t) cc_final: 0.9470 (p) REVERT: B 84 MET cc_start: 0.9403 (mmt) cc_final: 0.8448 (mmp) REVERT: B 88 TYR cc_start: 0.9481 (m-10) cc_final: 0.9241 (m-80) REVERT: B 97 LEU cc_start: 0.9271 (tp) cc_final: 0.8359 (tp) REVERT: C 25 PHE cc_start: 0.7986 (m-10) cc_final: 0.7643 (m-10) REVERT: C 39 TYR cc_start: 0.8910 (m-80) cc_final: 0.8172 (m-80) REVERT: C 56 GLU cc_start: 0.9195 (pp20) cc_final: 0.8499 (tt0) REVERT: C 68 ASN cc_start: 0.8857 (m-40) cc_final: 0.8646 (m110) REVERT: C 83 LEU cc_start: 0.9756 (mt) cc_final: 0.9489 (mt) REVERT: C 91 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9005 (mp0) REVERT: C 93 LEU cc_start: 0.9648 (mt) cc_final: 0.9343 (mt) REVERT: C 110 ASN cc_start: 0.9400 (t0) cc_final: 0.9029 (m110) REVERT: C 111 ILE cc_start: 0.9305 (mt) cc_final: 0.9084 (mm) REVERT: D 34 TYR cc_start: 0.9077 (m-80) cc_final: 0.8831 (m-80) REVERT: D 40 LYS cc_start: 0.9527 (mttt) cc_final: 0.9110 (mtmm) REVERT: D 64 ASN cc_start: 0.9556 (m-40) cc_final: 0.8793 (t0) REVERT: D 96 ARG cc_start: 0.9125 (mtp180) cc_final: 0.8885 (mtm180) REVERT: D 103 LEU cc_start: 0.9523 (mt) cc_final: 0.9246 (mt) REVERT: E 39 HIS cc_start: 0.8386 (m90) cc_final: 0.7916 (m90) REVERT: E 41 TYR cc_start: 0.8518 (m-80) cc_final: 0.8215 (m-80) REVERT: E 74 ILE cc_start: 0.9693 (mt) cc_final: 0.9346 (tt) REVERT: E 93 GLN cc_start: 0.9416 (tt0) cc_final: 0.9137 (tt0) REVERT: E 99 TYR cc_start: 0.9451 (t80) cc_final: 0.9108 (t80) REVERT: E 117 VAL cc_start: 0.9621 (OUTLIER) cc_final: 0.9272 (p) REVERT: F 35 ARG cc_start: 0.9746 (ttm170) cc_final: 0.9431 (ttm110) REVERT: F 49 LEU cc_start: 0.9766 (mm) cc_final: 0.9461 (tt) REVERT: F 53 GLU cc_start: 0.9140 (tp30) cc_final: 0.8529 (tp30) REVERT: F 54 THR cc_start: 0.9664 (m) cc_final: 0.9426 (p) REVERT: F 59 LYS cc_start: 0.9783 (tttm) cc_final: 0.9460 (tppp) REVERT: F 64 ASN cc_start: 0.9660 (m-40) cc_final: 0.9010 (t0) REVERT: F 84 MET cc_start: 0.9256 (mmm) cc_final: 0.8371 (mmm) REVERT: F 85 ASP cc_start: 0.9078 (m-30) cc_final: 0.8740 (t70) REVERT: G 25 PHE cc_start: 0.9254 (m-80) cc_final: 0.8606 (m-10) REVERT: G 27 VAL cc_start: 0.8578 (m) cc_final: 0.8258 (p) REVERT: G 39 TYR cc_start: 0.9000 (m-80) cc_final: 0.8666 (m-80) REVERT: G 84 GLN cc_start: 0.9400 (tp40) cc_final: 0.9180 (tp40) REVERT: G 89 ASN cc_start: 0.9649 (m-40) cc_final: 0.9425 (m110) REVERT: G 94 ASN cc_start: 0.9700 (t0) cc_final: 0.9321 (m110) REVERT: G 95 LYS cc_start: 0.9631 (mttt) cc_final: 0.9426 (mttt) REVERT: G 101 THR cc_start: 0.9688 (m) cc_final: 0.9360 (p) REVERT: G 102 ILE cc_start: 0.9641 (mt) cc_final: 0.9310 (mt) REVERT: G 107 VAL cc_start: 0.8488 (t) cc_final: 0.8168 (m) REVERT: H 34 TYR cc_start: 0.9633 (m-80) cc_final: 0.9218 (m-10) REVERT: H 59 MET cc_start: 0.9617 (mmm) cc_final: 0.9205 (mmm) REVERT: H 68 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9230 (tm-30) REVERT: H 73 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8920 (mm-30) REVERT: H 103 LEU cc_start: 0.9700 (mt) cc_final: 0.9469 (mt) REVERT: S 103 CYS cc_start: 0.5620 (t) cc_final: 0.5356 (t) REVERT: S 203 ASN cc_start: 0.9452 (t0) cc_final: 0.9093 (m-40) REVERT: S 276 LEU cc_start: 0.9569 (tp) cc_final: 0.9250 (pt) REVERT: S 278 MET cc_start: 0.6685 (mmm) cc_final: 0.6442 (mmm) outliers start: 4 outliers final: 0 residues processed: 385 average time/residue: 0.1499 time to fit residues: 78.5738 Evaluate side-chains 239 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C -32 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 25 ASN G 24 GLN G 38 ASN H 60 ASN H 106 HIS ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 215 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.040278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.027396 restraints weight = 133052.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028289 restraints weight = 74417.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.028876 restraints weight = 52845.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.029224 restraints weight = 42944.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.029439 restraints weight = 38050.358| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15173 Z= 0.316 Angle : 0.759 18.843 21720 Z= 0.412 Chirality : 0.041 0.171 2447 Planarity : 0.006 0.053 1760 Dihedral : 30.553 171.430 4337 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.34 % Allowed : 4.75 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1033 helix: 1.31 (0.21), residues: 578 sheet: -0.82 (0.61), residues: 67 loop : -1.25 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 29 TYR 0.027 0.002 TYR D 80 PHE 0.016 0.002 PHE A 84 TRP 0.008 0.002 TRP S 135 HIS 0.012 0.003 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00676 (15161) covalent geometry : angle 0.69794 (21702) hydrogen bonds : bond 0.08135 ( 834) hydrogen bonds : angle 4.00531 ( 2077) metal coordination : bond 0.01378 ( 12) metal coordination : angle 10.36038 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 281 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8284 (mm) cc_final: 0.7988 (mm) REVERT: A 64 LYS cc_start: 0.9600 (mppt) cc_final: 0.9295 (mmtm) REVERT: A 65 LEU cc_start: 0.9734 (mm) cc_final: 0.9533 (tp) REVERT: A 68 GLN cc_start: 0.9780 (tt0) cc_final: 0.9291 (tm-30) REVERT: A 80 THR cc_start: 0.9332 (m) cc_final: 0.9117 (p) REVERT: A 90 MET cc_start: 0.9690 (tpt) cc_final: 0.9387 (tpt) REVERT: A 120 MET cc_start: 0.9434 (tpt) cc_final: 0.9128 (tpp) REVERT: B 44 LYS cc_start: 0.9524 (tttt) cc_final: 0.9242 (ttpt) REVERT: B 84 MET cc_start: 0.9328 (mmt) cc_final: 0.8199 (mmm) REVERT: B 85 ASP cc_start: 0.9019 (m-30) cc_final: 0.8621 (t70) REVERT: B 88 TYR cc_start: 0.9388 (m-10) cc_final: 0.8819 (m-80) REVERT: C 39 TYR cc_start: 0.8991 (m-80) cc_final: 0.8531 (m-80) REVERT: C 90 ASP cc_start: 0.8740 (t70) cc_final: 0.8303 (t0) REVERT: C 91 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8812 (mp0) REVERT: C 96 LEU cc_start: 0.9111 (mt) cc_final: 0.8715 (mt) REVERT: C 110 ASN cc_start: 0.9451 (t0) cc_final: 0.8934 (m110) REVERT: C 111 ILE cc_start: 0.9336 (mt) cc_final: 0.9082 (mm) REVERT: C 112 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8009 (tm-30) REVERT: D 54 LYS cc_start: 0.9600 (mppt) cc_final: 0.9300 (mppt) REVERT: D 64 ASN cc_start: 0.9492 (m-40) cc_final: 0.9046 (t0) REVERT: D 68 GLU cc_start: 0.9240 (mp0) cc_final: 0.8623 (mm-30) REVERT: D 103 LEU cc_start: 0.9643 (mt) cc_final: 0.9360 (mt) REVERT: E 36 MET cc_start: 0.9364 (mtm) cc_final: 0.8866 (mtt) REVERT: E 39 HIS cc_start: 0.8393 (m90) cc_final: 0.7954 (m90) REVERT: E 56 LYS cc_start: 0.9406 (pttt) cc_final: 0.9085 (pptt) REVERT: E 73 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9187 (mm-30) REVERT: E 94 GLU cc_start: 0.8981 (tp30) cc_final: 0.8492 (tm-30) REVERT: E 103 LEU cc_start: 0.9644 (mt) cc_final: 0.9391 (mt) REVERT: E 120 MET cc_start: 0.9451 (mmp) cc_final: 0.8727 (mmm) REVERT: F 31 LYS cc_start: 0.9745 (ttpt) cc_final: 0.9454 (ttpp) REVERT: F 35 ARG cc_start: 0.9713 (ttm170) cc_final: 0.9402 (ttm110) REVERT: F 37 LEU cc_start: 0.9895 (mm) cc_final: 0.9626 (mm) REVERT: F 49 LEU cc_start: 0.9746 (mm) cc_final: 0.8741 (tp) REVERT: F 54 THR cc_start: 0.9737 (m) cc_final: 0.9468 (p) REVERT: F 59 LYS cc_start: 0.9801 (tttm) cc_final: 0.9581 (tppp) REVERT: F 62 LEU cc_start: 0.9844 (mt) cc_final: 0.9632 (mt) REVERT: F 64 ASN cc_start: 0.9663 (m-40) cc_final: 0.9441 (t0) REVERT: F 68 ASP cc_start: 0.9231 (m-30) cc_final: 0.8797 (m-30) REVERT: F 85 ASP cc_start: 0.9256 (m-30) cc_final: 0.8932 (m-30) REVERT: G 61 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9055 (mm-30) REVERT: G 78 ILE cc_start: 0.9825 (mm) cc_final: 0.9462 (tp) REVERT: G 92 GLU cc_start: 0.9064 (mp0) cc_final: 0.8500 (mt-10) REVERT: G 94 ASN cc_start: 0.9759 (t0) cc_final: 0.9343 (m110) REVERT: H 59 MET cc_start: 0.9522 (mmm) cc_final: 0.9073 (mmp) REVERT: H 68 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9039 (tm-30) REVERT: H 76 ARG cc_start: 0.8858 (ptp90) cc_final: 0.8457 (ptp90) REVERT: H 103 LEU cc_start: 0.9606 (mt) cc_final: 0.9254 (mt) REVERT: S 103 CYS cc_start: 0.5771 (t) cc_final: 0.5567 (t) REVERT: S 203 ASN cc_start: 0.9618 (t0) cc_final: 0.9268 (m-40) REVERT: S 223 MET cc_start: 0.8228 (tmm) cc_final: 0.7990 (tmm) REVERT: S 276 LEU cc_start: 0.9514 (tp) cc_final: 0.9194 (tp) outliers start: 3 outliers final: 0 residues processed: 283 average time/residue: 0.1384 time to fit residues: 54.4318 Evaluate side-chains 206 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 60 ASN H 92 GLN S 164 ASN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.039452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.026691 restraints weight = 135776.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.027545 restraints weight = 77225.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.028128 restraints weight = 55655.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028430 restraints weight = 45662.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028668 restraints weight = 40978.482| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15173 Z= 0.279 Angle : 0.700 15.305 21720 Z= 0.387 Chirality : 0.039 0.155 2447 Planarity : 0.005 0.055 1760 Dihedral : 31.045 179.593 4337 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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 are not related in a simple way. whole: 0.43 (0.26), residues: 1033 helix: 1.31 (0.21), residues: 572 sheet: -0.93 (0.61), residues: 68 loop : -0.99 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 27 TYR 0.027 0.002 TYR F 88 PHE 0.013 0.002 PHE A 84 TRP 0.005 0.002 TRP S 135 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00595 (15161) covalent geometry : angle 0.65187 (21702) hydrogen bonds : bond 0.07100 ( 834) hydrogen bonds : angle 3.91380 ( 2077) metal coordination : bond 0.01339 ( 12) metal coordination : angle 8.90643 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9626 (mppt) cc_final: 0.9264 (mmtm) REVERT: A 68 GLN cc_start: 0.9764 (tt0) cc_final: 0.9249 (tm-30) REVERT: A 81 ASP cc_start: 0.8690 (t70) cc_final: 0.8422 (t0) REVERT: A 90 MET cc_start: 0.9690 (tpt) cc_final: 0.9442 (tpp) REVERT: A 93 GLN cc_start: 0.9253 (tt0) cc_final: 0.8878 (tp-100) REVERT: A 94 GLU cc_start: 0.8722 (tp30) cc_final: 0.8132 (tm-30) REVERT: A 97 GLU cc_start: 0.9173 (pp20) cc_final: 0.8891 (pp20) REVERT: A 105 GLU cc_start: 0.9181 (tp30) cc_final: 0.8752 (tm-30) REVERT: B 44 LYS cc_start: 0.9500 (tttt) cc_final: 0.9201 (ttpt) REVERT: B 59 LYS cc_start: 0.9493 (ttpp) cc_final: 0.9261 (tmmt) REVERT: B 64 ASN cc_start: 0.9665 (m-40) cc_final: 0.9252 (t0) REVERT: B 68 ASP cc_start: 0.9554 (m-30) cc_final: 0.9317 (m-30) REVERT: B 84 MET cc_start: 0.9442 (mmt) cc_final: 0.9194 (mmm) REVERT: B 85 ASP cc_start: 0.9020 (m-30) cc_final: 0.8512 (t0) REVERT: B 88 TYR cc_start: 0.9553 (m-10) cc_final: 0.9307 (m-80) REVERT: B 97 LEU cc_start: 0.9174 (tt) cc_final: 0.8387 (tp) REVERT: C 39 TYR cc_start: 0.9145 (m-80) cc_final: 0.8367 (m-80) REVERT: C 90 ASP cc_start: 0.8969 (t70) cc_final: 0.8578 (t0) REVERT: C 91 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8841 (mp0) REVERT: C 96 LEU cc_start: 0.9278 (mt) cc_final: 0.9012 (mt) REVERT: C 110 ASN cc_start: 0.9511 (t0) cc_final: 0.8955 (m110) REVERT: C 111 ILE cc_start: 0.9336 (mt) cc_final: 0.9036 (mm) REVERT: D 40 LYS cc_start: 0.9450 (mttt) cc_final: 0.9183 (ptpt) REVERT: D 56 MET cc_start: 0.9618 (tpp) cc_final: 0.9353 (tpp) REVERT: D 64 ASN cc_start: 0.9463 (m-40) cc_final: 0.8797 (t0) REVERT: D 68 GLU cc_start: 0.9261 (mp0) cc_final: 0.8322 (mp0) REVERT: D 103 LEU cc_start: 0.9734 (mt) cc_final: 0.9484 (mt) REVERT: E 36 MET cc_start: 0.9425 (mtm) cc_final: 0.8832 (mtt) REVERT: E 39 HIS cc_start: 0.8328 (m90) cc_final: 0.7843 (m90) REVERT: E 73 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9053 (mm-30) REVERT: E 79 LYS cc_start: 0.9664 (mmmm) cc_final: 0.9335 (tptp) REVERT: E 93 GLN cc_start: 0.9283 (mt0) cc_final: 0.8962 (mp10) REVERT: E 120 MET cc_start: 0.9398 (mmp) cc_final: 0.8847 (mmm) REVERT: F 31 LYS cc_start: 0.9732 (ttpt) cc_final: 0.9338 (ttpp) REVERT: F 35 ARG cc_start: 0.9689 (ttm170) cc_final: 0.9300 (ttm110) REVERT: F 37 LEU cc_start: 0.9867 (mm) cc_final: 0.9635 (mm) REVERT: F 44 LYS cc_start: 0.9287 (ttmt) cc_final: 0.8824 (mttt) REVERT: F 49 LEU cc_start: 0.9651 (mm) cc_final: 0.9276 (tp) REVERT: F 54 THR cc_start: 0.9730 (m) cc_final: 0.9448 (p) REVERT: F 63 GLU cc_start: 0.9599 (mt-10) cc_final: 0.9287 (mt-10) REVERT: F 68 ASP cc_start: 0.9038 (m-30) cc_final: 0.8693 (m-30) REVERT: F 85 ASP cc_start: 0.9277 (m-30) cc_final: 0.8997 (m-30) REVERT: F 98 TYR cc_start: 0.8891 (m-80) cc_final: 0.8656 (m-80) REVERT: G 25 PHE cc_start: 0.9282 (m-80) cc_final: 0.9063 (m-10) REVERT: G 61 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9126 (mm-30) REVERT: G 92 GLU cc_start: 0.9164 (mp0) cc_final: 0.8737 (mt-10) REVERT: G 94 ASN cc_start: 0.9756 (t0) cc_final: 0.9352 (m-40) REVERT: G 95 LYS cc_start: 0.9427 (mtmm) cc_final: 0.9209 (mttp) REVERT: G 101 THR cc_start: 0.9105 (p) cc_final: 0.8810 (p) REVERT: H 34 TYR cc_start: 0.9642 (m-80) cc_final: 0.9230 (m-10) REVERT: H 59 MET cc_start: 0.9657 (mmm) cc_final: 0.9170 (mmp) REVERT: S 103 CYS cc_start: 0.6180 (t) cc_final: 0.5928 (t) REVERT: S 203 ASN cc_start: 0.9692 (t0) cc_final: 0.9366 (m-40) REVERT: S 223 MET cc_start: 0.8414 (tmm) cc_final: 0.8072 (tmm) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1303 time to fit residues: 47.2893 Evaluate side-chains 199 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.039757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.027068 restraints weight = 136274.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.027929 restraints weight = 76578.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028499 restraints weight = 54845.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.028847 restraints weight = 44636.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.029013 restraints weight = 39748.326| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15173 Z= 0.230 Angle : 0.654 12.938 21720 Z= 0.366 Chirality : 0.038 0.165 2447 Planarity : 0.005 0.057 1760 Dihedral : 30.900 178.270 4337 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 are not related in a simple way. whole: 0.53 (0.26), residues: 1033 helix: 1.31 (0.21), residues: 573 sheet: -0.78 (0.61), residues: 67 loop : -0.83 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 52 TYR 0.044 0.002 TYR F 88 PHE 0.012 0.001 PHE C 25 TRP 0.005 0.002 TRP S 270 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00496 (15161) covalent geometry : angle 0.61508 (21702) hydrogen bonds : bond 0.06049 ( 834) hydrogen bonds : angle 3.83233 ( 2077) metal coordination : bond 0.00990 ( 12) metal coordination : angle 7.75961 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8466 (mm) cc_final: 0.7943 (mm) REVERT: A 64 LYS cc_start: 0.9657 (mppt) cc_final: 0.9351 (mmtm) REVERT: A 65 LEU cc_start: 0.9720 (mm) cc_final: 0.9467 (tp) REVERT: A 68 GLN cc_start: 0.9760 (tt0) cc_final: 0.9202 (tm-30) REVERT: A 81 ASP cc_start: 0.8680 (t70) cc_final: 0.8458 (t0) REVERT: A 87 SER cc_start: 0.9653 (m) cc_final: 0.9323 (p) REVERT: A 90 MET cc_start: 0.9685 (tpt) cc_final: 0.9417 (tpp) REVERT: A 94 GLU cc_start: 0.8719 (tp30) cc_final: 0.8088 (tm-30) REVERT: A 97 GLU cc_start: 0.9128 (pp20) cc_final: 0.8861 (pp20) REVERT: A 120 MET cc_start: 0.9597 (tpp) cc_final: 0.9166 (tpp) REVERT: B 44 LYS cc_start: 0.9490 (tttt) cc_final: 0.9173 (ttpt) REVERT: B 59 LYS cc_start: 0.9487 (ttpp) cc_final: 0.9250 (tmmt) REVERT: B 85 ASP cc_start: 0.9112 (m-30) cc_final: 0.8735 (t0) REVERT: B 97 LEU cc_start: 0.9098 (tt) cc_final: 0.8670 (tt) REVERT: C 39 TYR cc_start: 0.9090 (m-80) cc_final: 0.8731 (m-80) REVERT: C 56 GLU cc_start: 0.9261 (pp20) cc_final: 0.9011 (pp20) REVERT: C 83 LEU cc_start: 0.9524 (mp) cc_final: 0.9281 (mp) REVERT: C 90 ASP cc_start: 0.9062 (t70) cc_final: 0.8402 (t0) REVERT: C 110 ASN cc_start: 0.9466 (t0) cc_final: 0.8925 (m110) REVERT: D 56 MET cc_start: 0.9578 (tpp) cc_final: 0.9356 (tpp) REVERT: D 64 ASN cc_start: 0.9353 (m-40) cc_final: 0.8687 (t0) REVERT: D 68 GLU cc_start: 0.9298 (mp0) cc_final: 0.8516 (mp0) REVERT: D 96 ARG cc_start: 0.9255 (mtm-85) cc_final: 0.8610 (mtm-85) REVERT: E 36 MET cc_start: 0.9340 (mtm) cc_final: 0.8831 (mtt) REVERT: E 39 HIS cc_start: 0.8330 (m90) cc_final: 0.7877 (m90) REVERT: E 73 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9066 (mm-30) REVERT: E 79 LYS cc_start: 0.9655 (mmmm) cc_final: 0.9312 (tmtt) REVERT: E 86 SER cc_start: 0.9542 (p) cc_final: 0.9195 (p) REVERT: E 103 LEU cc_start: 0.9565 (mt) cc_final: 0.9362 (mt) REVERT: E 120 MET cc_start: 0.9428 (mmp) cc_final: 0.8897 (mmm) REVERT: F 35 ARG cc_start: 0.9702 (ttm170) cc_final: 0.9432 (ttm110) REVERT: F 63 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9258 (mt-10) REVERT: F 85 ASP cc_start: 0.9281 (m-30) cc_final: 0.8997 (m-30) REVERT: F 98 TYR cc_start: 0.8902 (m-80) cc_final: 0.8504 (m-80) REVERT: G 61 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9117 (mm-30) REVERT: G 92 GLU cc_start: 0.9101 (mp0) cc_final: 0.8757 (mt-10) REVERT: G 94 ASN cc_start: 0.9735 (t0) cc_final: 0.9363 (m-40) REVERT: H 34 TYR cc_start: 0.9719 (m-80) cc_final: 0.9262 (m-10) REVERT: H 59 MET cc_start: 0.9644 (mmm) cc_final: 0.9163 (mmp) REVERT: H 103 LEU cc_start: 0.9591 (mt) cc_final: 0.9342 (mt) REVERT: S 103 CYS cc_start: 0.6386 (t) cc_final: 0.6150 (t) REVERT: S 203 ASN cc_start: 0.9693 (t0) cc_final: 0.9376 (m-40) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1285 time to fit residues: 45.2631 Evaluate side-chains 201 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 0.0970 chunk 102 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 23 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 128 optimal weight: 0.2980 overall best weight: 3.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.039504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.026977 restraints weight = 138435.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027838 restraints weight = 79535.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.028327 restraints weight = 57326.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.028685 restraints weight = 47913.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028868 restraints weight = 42774.559| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15173 Z= 0.206 Angle : 0.633 11.529 21720 Z= 0.356 Chirality : 0.037 0.151 2447 Planarity : 0.004 0.056 1760 Dihedral : 30.911 178.220 4337 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.11 % Allowed : 2.26 % Favored : 97.63 % 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 are not related in a simple way. whole: 0.61 (0.27), residues: 1033 helix: 1.31 (0.22), residues: 576 sheet: -0.68 (0.61), residues: 66 loop : -0.69 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.044 0.002 TYR F 88 PHE 0.010 0.001 PHE C 25 TRP 0.004 0.001 TRP S 270 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (15161) covalent geometry : angle 0.59853 (21702) hydrogen bonds : bond 0.05496 ( 834) hydrogen bonds : angle 3.76545 ( 2077) metal coordination : bond 0.00885 ( 12) metal coordination : angle 7.14342 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8474 (mm) cc_final: 0.8057 (mm) REVERT: A 64 LYS cc_start: 0.9618 (mppt) cc_final: 0.9323 (mmtm) REVERT: A 65 LEU cc_start: 0.9713 (mm) cc_final: 0.9461 (tp) REVERT: A 68 GLN cc_start: 0.9748 (tt0) cc_final: 0.9186 (tm-30) REVERT: A 87 SER cc_start: 0.9660 (m) cc_final: 0.9334 (p) REVERT: A 90 MET cc_start: 0.9685 (tpt) cc_final: 0.9433 (tpp) REVERT: A 94 GLU cc_start: 0.8679 (tp30) cc_final: 0.8072 (tm-30) REVERT: A 97 GLU cc_start: 0.9103 (pp20) cc_final: 0.8857 (pp20) REVERT: A 106 ASP cc_start: 0.9373 (m-30) cc_final: 0.7975 (m-30) REVERT: A 120 MET cc_start: 0.9624 (tpp) cc_final: 0.9153 (tpp) REVERT: B 44 LYS cc_start: 0.9460 (tttt) cc_final: 0.9216 (ttmm) REVERT: B 59 LYS cc_start: 0.9506 (ttpp) cc_final: 0.9275 (tmmt) REVERT: B 85 ASP cc_start: 0.9101 (m-30) cc_final: 0.8640 (t0) REVERT: B 97 LEU cc_start: 0.9078 (tt) cc_final: 0.8704 (tt) REVERT: C 39 TYR cc_start: 0.9146 (m-80) cc_final: 0.8683 (m-80) REVERT: C 56 GLU cc_start: 0.9232 (pp20) cc_final: 0.8940 (pp20) REVERT: C 62 ILE cc_start: 0.9596 (pt) cc_final: 0.9378 (pt) REVERT: C 83 LEU cc_start: 0.9516 (mp) cc_final: 0.9272 (mp) REVERT: C 90 ASP cc_start: 0.9112 (t70) cc_final: 0.8453 (t0) REVERT: C 110 ASN cc_start: 0.9462 (t0) cc_final: 0.8995 (m110) REVERT: C 111 ILE cc_start: 0.9269 (mp) cc_final: 0.8824 (mm) REVERT: D 59 MET cc_start: 0.9618 (mmp) cc_final: 0.9325 (mmm) REVERT: D 64 ASN cc_start: 0.9411 (m-40) cc_final: 0.8919 (t0) REVERT: D 68 GLU cc_start: 0.9237 (mp0) cc_final: 0.8577 (mm-30) REVERT: D 96 ARG cc_start: 0.9150 (mtm-85) cc_final: 0.8682 (mtm-85) REVERT: E 36 MET cc_start: 0.9307 (mtm) cc_final: 0.8765 (mtt) REVERT: E 39 HIS cc_start: 0.8339 (m90) cc_final: 0.7799 (m90) REVERT: E 62 ILE cc_start: 0.8959 (tp) cc_final: 0.8357 (tp) REVERT: E 73 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9018 (mm-30) REVERT: E 79 LYS cc_start: 0.9671 (mmmm) cc_final: 0.9337 (tmtt) REVERT: E 86 SER cc_start: 0.9474 (p) cc_final: 0.9022 (p) REVERT: E 90 MET cc_start: 0.9519 (mmp) cc_final: 0.9186 (mmp) REVERT: E 103 LEU cc_start: 0.9561 (mt) cc_final: 0.9266 (mt) REVERT: E 120 MET cc_start: 0.9400 (mmp) cc_final: 0.8901 (mmm) REVERT: F 44 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8722 (mtmt) REVERT: F 63 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9237 (mt-10) REVERT: F 64 ASN cc_start: 0.9439 (t0) cc_final: 0.9148 (t0) REVERT: F 84 MET cc_start: 0.9567 (mmm) cc_final: 0.9357 (mmm) REVERT: F 85 ASP cc_start: 0.9271 (m-30) cc_final: 0.8987 (m-30) REVERT: G 61 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9129 (mm-30) REVERT: G 94 ASN cc_start: 0.9640 (t0) cc_final: 0.9190 (m-40) REVERT: H 34 TYR cc_start: 0.9650 (m-80) cc_final: 0.9382 (m-80) REVERT: H 59 MET cc_start: 0.9641 (mmm) cc_final: 0.9177 (mmp) REVERT: H 103 LEU cc_start: 0.9531 (mt) cc_final: 0.9290 (mt) REVERT: S 103 CYS cc_start: 0.6334 (t) cc_final: 0.6108 (t) REVERT: S 203 ASN cc_start: 0.9692 (t0) cc_final: 0.9370 (m-40) REVERT: S 306 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5444 (pp30) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.1314 time to fit residues: 47.0334 Evaluate side-chains 197 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 116 optimal weight: 40.0000 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.039316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.026590 restraints weight = 139887.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027433 restraints weight = 80707.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.027987 restraints weight = 58388.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028271 restraints weight = 48419.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.028514 restraints weight = 43612.204| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15173 Z= 0.233 Angle : 0.662 14.170 21720 Z= 0.369 Chirality : 0.038 0.172 2447 Planarity : 0.005 0.056 1760 Dihedral : 31.010 177.518 4337 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 are not related in a simple way. whole: 0.41 (0.26), residues: 1033 helix: 1.14 (0.21), residues: 576 sheet: -0.85 (0.56), residues: 78 loop : -0.73 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.041 0.002 TYR F 88 PHE 0.018 0.002 PHE E 67 TRP 0.008 0.002 TRP S 270 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00505 (15161) covalent geometry : angle 0.61775 (21702) hydrogen bonds : bond 0.06508 ( 834) hydrogen bonds : angle 3.93703 ( 2077) metal coordination : bond 0.01163 ( 12) metal coordination : angle 8.24192 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8532 (mm) cc_final: 0.7901 (pp) REVERT: A 68 GLN cc_start: 0.9762 (tt0) cc_final: 0.9234 (tm-30) REVERT: A 87 SER cc_start: 0.9703 (m) cc_final: 0.9419 (p) REVERT: A 90 MET cc_start: 0.9699 (tpt) cc_final: 0.9458 (tpp) REVERT: A 99 TYR cc_start: 0.9552 (t80) cc_final: 0.9348 (t80) REVERT: A 106 ASP cc_start: 0.8955 (m-30) cc_final: 0.8489 (m-30) REVERT: A 120 MET cc_start: 0.9683 (tpp) cc_final: 0.9243 (tpp) REVERT: B 44 LYS cc_start: 0.9434 (tttt) cc_final: 0.9174 (ttmm) REVERT: B 97 LEU cc_start: 0.9106 (tt) cc_final: 0.8351 (tp) REVERT: C 39 TYR cc_start: 0.9188 (m-80) cc_final: 0.8801 (m-80) REVERT: C 56 GLU cc_start: 0.9211 (pp20) cc_final: 0.8987 (pp20) REVERT: C 83 LEU cc_start: 0.9577 (mp) cc_final: 0.9315 (mp) REVERT: C 90 ASP cc_start: 0.9133 (t70) cc_final: 0.8491 (t0) REVERT: C 110 ASN cc_start: 0.9481 (t0) cc_final: 0.8928 (m110) REVERT: C 111 ILE cc_start: 0.9317 (mp) cc_final: 0.8836 (mm) REVERT: D 59 MET cc_start: 0.9645 (mmp) cc_final: 0.9384 (mmm) REVERT: D 64 ASN cc_start: 0.9299 (m-40) cc_final: 0.9025 (t0) REVERT: E 36 MET cc_start: 0.9286 (mtm) cc_final: 0.8725 (mtt) REVERT: E 39 HIS cc_start: 0.8328 (m90) cc_final: 0.7783 (m90) REVERT: E 56 LYS cc_start: 0.9356 (pptt) cc_final: 0.9088 (pptt) REVERT: E 67 PHE cc_start: 0.9609 (t80) cc_final: 0.9406 (t80) REVERT: E 73 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8959 (mm-30) REVERT: E 79 LYS cc_start: 0.9691 (mmmm) cc_final: 0.9315 (tmtt) REVERT: E 86 SER cc_start: 0.9459 (p) cc_final: 0.9163 (p) REVERT: E 106 ASP cc_start: 0.9117 (m-30) cc_final: 0.8839 (m-30) REVERT: E 120 MET cc_start: 0.9351 (mmp) cc_final: 0.8870 (mmm) REVERT: F 44 LYS cc_start: 0.9251 (ttmt) cc_final: 0.8766 (mttt) REVERT: F 64 ASN cc_start: 0.9441 (t0) cc_final: 0.9149 (t0) REVERT: F 84 MET cc_start: 0.9575 (mmm) cc_final: 0.9359 (mmm) REVERT: F 85 ASP cc_start: 0.9309 (m-30) cc_final: 0.9051 (m-30) REVERT: G 61 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9120 (mm-30) REVERT: G 94 ASN cc_start: 0.9611 (t0) cc_final: 0.9176 (m-40) REVERT: G 101 THR cc_start: 0.9037 (p) cc_final: 0.8743 (p) REVERT: H 59 MET cc_start: 0.9627 (mmm) cc_final: 0.9231 (mmp) REVERT: H 76 ARG cc_start: 0.8983 (ptp90) cc_final: 0.8625 (ptp90) REVERT: H 99 LEU cc_start: 0.9066 (mt) cc_final: 0.8848 (mt) REVERT: H 102 GLU cc_start: 0.9300 (tp30) cc_final: 0.8878 (tm-30) REVERT: S 203 ASN cc_start: 0.9725 (t0) cc_final: 0.9400 (m-40) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1237 time to fit residues: 44.3898 Evaluate side-chains 188 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 0.0570 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.039027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.026457 restraints weight = 139481.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.027245 restraints weight = 81871.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027790 restraints weight = 59185.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.028123 restraints weight = 49107.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.028224 restraints weight = 43839.294| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15173 Z= 0.225 Angle : 0.663 14.909 21720 Z= 0.370 Chirality : 0.038 0.182 2447 Planarity : 0.005 0.056 1760 Dihedral : 31.059 177.369 4337 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 are not related in a simple way. whole: 0.22 (0.27), residues: 1033 helix: 0.94 (0.21), residues: 575 sheet: -0.93 (0.57), residues: 78 loop : -0.73 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.040 0.002 TYR F 88 PHE 0.014 0.001 PHE H 62 TRP 0.007 0.002 TRP S 270 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00489 (15161) covalent geometry : angle 0.62199 (21702) hydrogen bonds : bond 0.06097 ( 834) hydrogen bonds : angle 4.02914 ( 2077) metal coordination : bond 0.01094 ( 12) metal coordination : angle 7.96702 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9434 (mp0) cc_final: 0.9043 (mp0) REVERT: A 65 LEU cc_start: 0.9711 (mm) cc_final: 0.9441 (tp) REVERT: A 68 GLN cc_start: 0.9745 (tt0) cc_final: 0.9203 (tm-30) REVERT: A 87 SER cc_start: 0.9703 (m) cc_final: 0.9426 (p) REVERT: A 90 MET cc_start: 0.9670 (tpt) cc_final: 0.9403 (tpp) REVERT: A 97 GLU cc_start: 0.9003 (mp0) cc_final: 0.8789 (pm20) REVERT: A 105 GLU cc_start: 0.9025 (pp20) cc_final: 0.8765 (pp20) REVERT: A 106 ASP cc_start: 0.8964 (m-30) cc_final: 0.8444 (m-30) REVERT: A 120 MET cc_start: 0.9660 (tpp) cc_final: 0.9194 (tpp) REVERT: A 122 LYS cc_start: 0.9789 (ptpp) cc_final: 0.9586 (ptpp) REVERT: B 59 LYS cc_start: 0.9478 (pptt) cc_final: 0.8745 (pptt) REVERT: B 84 MET cc_start: 0.9435 (mmm) cc_final: 0.8941 (mmm) REVERT: B 88 TYR cc_start: 0.9624 (m-80) cc_final: 0.8921 (m-80) REVERT: C 39 TYR cc_start: 0.9191 (m-80) cc_final: 0.8681 (m-80) REVERT: C 56 GLU cc_start: 0.9246 (pp20) cc_final: 0.8996 (pp20) REVERT: C 83 LEU cc_start: 0.9582 (mp) cc_final: 0.9301 (mp) REVERT: C 90 ASP cc_start: 0.9144 (t70) cc_final: 0.8124 (t70) REVERT: C 92 GLU cc_start: 0.8837 (tt0) cc_final: 0.8563 (tp30) REVERT: C 93 LEU cc_start: 0.9615 (mt) cc_final: 0.9342 (mt) REVERT: D 56 MET cc_start: 0.9588 (tpp) cc_final: 0.9366 (tpp) REVERT: D 58 ILE cc_start: 0.9888 (mm) cc_final: 0.9657 (mm) REVERT: D 59 MET cc_start: 0.9624 (mmp) cc_final: 0.9335 (mmm) REVERT: D 64 ASN cc_start: 0.9312 (m-40) cc_final: 0.8945 (t0) REVERT: D 68 GLU cc_start: 0.9237 (mp0) cc_final: 0.8633 (mm-30) REVERT: E 36 MET cc_start: 0.9306 (mtm) cc_final: 0.8674 (mtt) REVERT: E 39 HIS cc_start: 0.8383 (m90) cc_final: 0.7854 (m90) REVERT: E 56 LYS cc_start: 0.9382 (pptt) cc_final: 0.9110 (pptt) REVERT: E 73 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8945 (mm-30) REVERT: E 79 LYS cc_start: 0.9711 (mmmm) cc_final: 0.9322 (tmtt) REVERT: E 86 SER cc_start: 0.9553 (p) cc_final: 0.9211 (p) REVERT: E 90 MET cc_start: 0.9557 (mmp) cc_final: 0.9209 (mmp) REVERT: E 106 ASP cc_start: 0.9474 (m-30) cc_final: 0.9271 (m-30) REVERT: E 115 LYS cc_start: 0.9441 (mppt) cc_final: 0.9240 (mptt) REVERT: E 120 MET cc_start: 0.9349 (mmp) cc_final: 0.8839 (mmm) REVERT: F 44 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8740 (mttt) REVERT: F 64 ASN cc_start: 0.9468 (t0) cc_final: 0.9183 (t0) REVERT: F 85 ASP cc_start: 0.9294 (m-30) cc_final: 0.9024 (m-30) REVERT: G 61 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9112 (mm-30) REVERT: G 94 ASN cc_start: 0.9603 (t0) cc_final: 0.9143 (m-40) REVERT: G 101 THR cc_start: 0.9024 (p) cc_final: 0.8751 (p) REVERT: H 31 LYS cc_start: 0.9196 (mptt) cc_final: 0.8869 (mmtm) REVERT: H 59 MET cc_start: 0.9676 (mmm) cc_final: 0.9223 (mmp) REVERT: H 76 ARG cc_start: 0.8998 (ptp90) cc_final: 0.8593 (ptp90) REVERT: H 102 GLU cc_start: 0.9324 (tp30) cc_final: 0.9035 (tp30) REVERT: S 203 ASN cc_start: 0.9723 (t0) cc_final: 0.9404 (m-40) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1177 time to fit residues: 41.6732 Evaluate side-chains 186 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 0.0670 chunk 106 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 111 optimal weight: 40.0000 chunk 64 optimal weight: 10.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.039351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026601 restraints weight = 139769.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.027450 restraints weight = 80745.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.028010 restraints weight = 58495.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.028366 restraints weight = 48047.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028481 restraints weight = 42920.755| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15173 Z= 0.209 Angle : 0.661 13.042 21720 Z= 0.370 Chirality : 0.038 0.198 2447 Planarity : 0.005 0.056 1760 Dihedral : 31.031 178.526 4337 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.11 % Allowed : 1.24 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 1033 helix: 0.97 (0.21), residues: 580 sheet: -0.93 (0.56), residues: 78 loop : -0.72 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 52 TYR 0.039 0.002 TYR F 88 PHE 0.025 0.002 PHE A 104 TRP 0.004 0.001 TRP S 270 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00453 (15161) covalent geometry : angle 0.62517 (21702) hydrogen bonds : bond 0.05735 ( 834) hydrogen bonds : angle 4.03512 ( 2077) metal coordination : bond 0.00917 ( 12) metal coordination : angle 7.46834 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9750 (tt0) cc_final: 0.9230 (tm-30) REVERT: A 87 SER cc_start: 0.9709 (m) cc_final: 0.9434 (p) REVERT: A 90 MET cc_start: 0.9660 (tpt) cc_final: 0.9453 (tpp) REVERT: A 97 GLU cc_start: 0.9140 (mp0) cc_final: 0.8728 (mp0) REVERT: A 105 GLU cc_start: 0.8968 (pp20) cc_final: 0.8707 (pp20) REVERT: A 106 ASP cc_start: 0.9028 (m-30) cc_final: 0.8562 (m-30) REVERT: A 108 ASN cc_start: 0.9643 (t0) cc_final: 0.9438 (m-40) REVERT: A 120 MET cc_start: 0.9652 (tpp) cc_final: 0.9306 (tpp) REVERT: B 43 VAL cc_start: 0.9292 (t) cc_final: 0.9061 (t) REVERT: B 64 ASN cc_start: 0.9630 (m-40) cc_final: 0.9330 (m110) REVERT: B 84 MET cc_start: 0.9458 (mmm) cc_final: 0.8918 (mmm) REVERT: B 88 TYR cc_start: 0.9631 (m-80) cc_final: 0.8914 (m-80) REVERT: C 39 TYR cc_start: 0.9195 (m-80) cc_final: 0.8661 (m-80) REVERT: C 56 GLU cc_start: 0.9204 (pp20) cc_final: 0.8971 (pp20) REVERT: C 83 LEU cc_start: 0.9569 (mp) cc_final: 0.9278 (mp) REVERT: C 84 GLN cc_start: 0.9495 (tp40) cc_final: 0.9259 (tm-30) REVERT: C 90 ASP cc_start: 0.9155 (t70) cc_final: 0.8042 (t70) REVERT: C 93 LEU cc_start: 0.9606 (mt) cc_final: 0.9230 (mt) REVERT: C 110 ASN cc_start: 0.9674 (t0) cc_final: 0.9318 (p0) REVERT: C 111 ILE cc_start: 0.9511 (mm) cc_final: 0.9287 (mm) REVERT: D 56 MET cc_start: 0.9606 (tpp) cc_final: 0.9379 (tpp) REVERT: D 59 MET cc_start: 0.9636 (mmp) cc_final: 0.9304 (mmm) REVERT: D 64 ASN cc_start: 0.9321 (m-40) cc_final: 0.8931 (t0) REVERT: D 68 GLU cc_start: 0.9235 (mp0) cc_final: 0.8611 (mm-30) REVERT: E 36 MET cc_start: 0.9241 (mtm) cc_final: 0.8975 (mpp) REVERT: E 39 HIS cc_start: 0.8068 (m90) cc_final: 0.7506 (m170) REVERT: E 73 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8634 (mm-30) REVERT: E 79 LYS cc_start: 0.9731 (mmmm) cc_final: 0.9382 (tmtt) REVERT: E 86 SER cc_start: 0.9603 (p) cc_final: 0.9374 (p) REVERT: E 90 MET cc_start: 0.9344 (mmp) cc_final: 0.8977 (mmp) REVERT: E 94 GLU cc_start: 0.8963 (mp0) cc_final: 0.8615 (mp0) REVERT: E 118 THR cc_start: 0.9134 (m) cc_final: 0.8568 (p) REVERT: E 120 MET cc_start: 0.9319 (mmp) cc_final: 0.8799 (mmm) REVERT: F 44 LYS cc_start: 0.9145 (ttmt) cc_final: 0.8776 (mtmt) REVERT: F 64 ASN cc_start: 0.9533 (t0) cc_final: 0.9275 (t0) REVERT: F 81 VAL cc_start: 0.9732 (t) cc_final: 0.9493 (t) REVERT: F 85 ASP cc_start: 0.9273 (m-30) cc_final: 0.9011 (m-30) REVERT: F 93 GLN cc_start: 0.8467 (mp10) cc_final: 0.8253 (mp10) REVERT: G 41 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8856 (mm-30) REVERT: G 61 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9103 (mm-30) REVERT: G 94 ASN cc_start: 0.9590 (t0) cc_final: 0.9141 (m-40) REVERT: G 101 THR cc_start: 0.9068 (p) cc_final: 0.8817 (p) REVERT: H 31 LYS cc_start: 0.9175 (mptt) cc_final: 0.8883 (mmtm) REVERT: H 59 MET cc_start: 0.9688 (mmm) cc_final: 0.9228 (mmp) REVERT: H 68 GLU cc_start: 0.9375 (tm-30) cc_final: 0.9158 (tm-30) REVERT: H 76 ARG cc_start: 0.9017 (ptp90) cc_final: 0.8620 (ptp90) REVERT: H 102 GLU cc_start: 0.9283 (tp30) cc_final: 0.8975 (tp30) REVERT: S 203 ASN cc_start: 0.9728 (t0) cc_final: 0.9416 (m-40) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1171 time to fit residues: 40.1860 Evaluate side-chains 187 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 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 = 0.3108 r_free = 0.3108 target = 0.037990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.025255 restraints weight = 143048.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.026065 restraints weight = 84657.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.026587 restraints weight = 62177.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.026919 restraints weight = 51798.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.027096 restraints weight = 46461.425| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15173 Z= 0.301 Angle : 0.720 13.897 21720 Z= 0.401 Chirality : 0.040 0.209 2447 Planarity : 0.005 0.075 1760 Dihedral : 31.425 177.682 4337 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % 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 are not related in a simple way. whole: 0.02 (0.27), residues: 1033 helix: 0.73 (0.21), residues: 584 sheet: -1.31 (0.57), residues: 73 loop : -0.70 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 52 TYR 0.038 0.002 TYR F 88 PHE 0.031 0.002 PHE A 67 TRP 0.007 0.002 TRP S 270 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00648 (15161) covalent geometry : angle 0.67602 (21702) hydrogen bonds : bond 0.08167 ( 834) hydrogen bonds : angle 4.42101 ( 2077) metal coordination : bond 0.01450 ( 12) metal coordination : angle 8.67108 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9367 (mp0) cc_final: 0.8965 (mp0) REVERT: A 68 GLN cc_start: 0.9746 (tt0) cc_final: 0.9192 (tm-30) REVERT: A 87 SER cc_start: 0.9741 (m) cc_final: 0.9483 (p) REVERT: A 90 MET cc_start: 0.9680 (tpt) cc_final: 0.9467 (tpp) REVERT: A 97 GLU cc_start: 0.9240 (mp0) cc_final: 0.8849 (mp0) REVERT: A 106 ASP cc_start: 0.9031 (m-30) cc_final: 0.8815 (m-30) REVERT: A 120 MET cc_start: 0.9680 (tpp) cc_final: 0.9323 (tpp) REVERT: B 64 ASN cc_start: 0.9638 (m-40) cc_final: 0.9340 (m110) REVERT: B 97 LEU cc_start: 0.9069 (tp) cc_final: 0.8854 (tp) REVERT: C 39 TYR cc_start: 0.9193 (m-80) cc_final: 0.8618 (m-80) REVERT: C 56 GLU cc_start: 0.9213 (pp20) cc_final: 0.8936 (pp20) REVERT: C 83 LEU cc_start: 0.9583 (mp) cc_final: 0.9367 (mt) REVERT: C 84 GLN cc_start: 0.9510 (tp40) cc_final: 0.9250 (tm-30) REVERT: C 99 ARG cc_start: 0.8781 (mtt180) cc_final: 0.8346 (mmm160) REVERT: C 110 ASN cc_start: 0.9670 (t0) cc_final: 0.9315 (p0) REVERT: C 111 ILE cc_start: 0.9526 (mm) cc_final: 0.9310 (mm) REVERT: D 56 MET cc_start: 0.9621 (tpp) cc_final: 0.9362 (tpp) REVERT: D 59 MET cc_start: 0.9634 (mmp) cc_final: 0.9343 (mmm) REVERT: D 64 ASN cc_start: 0.9301 (m-40) cc_final: 0.9026 (t0) REVERT: D 65 ASP cc_start: 0.9289 (t70) cc_final: 0.8906 (t70) REVERT: D 68 GLU cc_start: 0.9320 (mp0) cc_final: 0.8599 (mp0) REVERT: D 103 LEU cc_start: 0.9719 (mt) cc_final: 0.9514 (mt) REVERT: E 36 MET cc_start: 0.9293 (mtm) cc_final: 0.8906 (mpp) REVERT: E 39 HIS cc_start: 0.8277 (m90) cc_final: 0.7762 (m-70) REVERT: E 50 GLU cc_start: 0.9684 (mp0) cc_final: 0.9479 (pm20) REVERT: E 56 LYS cc_start: 0.9367 (pptt) cc_final: 0.9099 (pptt) REVERT: E 86 SER cc_start: 0.9560 (p) cc_final: 0.9278 (p) REVERT: E 90 MET cc_start: 0.9269 (mmp) cc_final: 0.8928 (mmp) REVERT: E 94 GLU cc_start: 0.8940 (mp0) cc_final: 0.8584 (mp0) REVERT: E 115 LYS cc_start: 0.9435 (mppt) cc_final: 0.9139 (mppt) REVERT: E 118 THR cc_start: 0.9120 (m) cc_final: 0.8612 (p) REVERT: E 120 MET cc_start: 0.9292 (mmp) cc_final: 0.8792 (mmm) REVERT: F 64 ASN cc_start: 0.9533 (t0) cc_final: 0.9159 (t0) REVERT: F 68 ASP cc_start: 0.9282 (m-30) cc_final: 0.8907 (m-30) REVERT: F 85 ASP cc_start: 0.9303 (m-30) cc_final: 0.9002 (m-30) REVERT: G 61 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9122 (mm-30) REVERT: G 94 ASN cc_start: 0.9580 (t0) cc_final: 0.9180 (t0) REVERT: G 101 THR cc_start: 0.9014 (p) cc_final: 0.8667 (p) REVERT: H 59 MET cc_start: 0.9676 (mmm) cc_final: 0.9213 (mmp) REVERT: H 102 GLU cc_start: 0.9297 (tp30) cc_final: 0.8944 (tp30) REVERT: S 203 ASN cc_start: 0.9719 (t0) cc_final: 0.9390 (m-40) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1198 time to fit residues: 37.8940 Evaluate side-chains 169 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.026186 restraints weight = 140557.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.027072 restraints weight = 82254.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.027605 restraints weight = 59727.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.027947 restraints weight = 49355.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028061 restraints weight = 44087.139| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15173 Z= 0.213 Angle : 0.698 13.311 21720 Z= 0.389 Chirality : 0.039 0.207 2447 Planarity : 0.005 0.058 1760 Dihedral : 31.299 178.670 4337 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % 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 are not related in a simple way. whole: 0.05 (0.27), residues: 1033 helix: 0.70 (0.21), residues: 583 sheet: -1.21 (0.58), residues: 73 loop : -0.61 (0.36), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 52 TYR 0.041 0.002 TYR F 88 PHE 0.017 0.002 PHE A 104 TRP 0.005 0.001 TRP S 270 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00462 (15161) covalent geometry : angle 0.65710 (21702) hydrogen bonds : bond 0.05801 ( 834) hydrogen bonds : angle 4.26564 ( 2077) metal coordination : bond 0.01008 ( 12) metal coordination : angle 8.16735 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9396 (mp0) cc_final: 0.8979 (mp0) REVERT: A 51 ILE cc_start: 0.9595 (mm) cc_final: 0.9381 (mm) REVERT: A 68 GLN cc_start: 0.9718 (tt0) cc_final: 0.9135 (tm-30) REVERT: A 87 SER cc_start: 0.9703 (m) cc_final: 0.9441 (p) REVERT: A 90 MET cc_start: 0.9704 (tpt) cc_final: 0.8627 (tpp) REVERT: A 106 ASP cc_start: 0.9452 (m-30) cc_final: 0.8760 (m-30) REVERT: A 120 MET cc_start: 0.9635 (tpp) cc_final: 0.9306 (tpp) REVERT: B 64 ASN cc_start: 0.9648 (m-40) cc_final: 0.9358 (m110) REVERT: B 84 MET cc_start: 0.9458 (mmm) cc_final: 0.9021 (mmm) REVERT: B 88 TYR cc_start: 0.9639 (m-80) cc_final: 0.8953 (m-80) REVERT: C 39 TYR cc_start: 0.9221 (m-80) cc_final: 0.8606 (m-80) REVERT: C 56 GLU cc_start: 0.9199 (pp20) cc_final: 0.8949 (pp20) REVERT: C 83 LEU cc_start: 0.9598 (mp) cc_final: 0.9296 (mp) REVERT: C 84 GLN cc_start: 0.9509 (tp40) cc_final: 0.9247 (tm-30) REVERT: C 90 ASP cc_start: 0.9151 (t70) cc_final: 0.8094 (t70) REVERT: C 93 LEU cc_start: 0.9628 (mt) cc_final: 0.9354 (mt) REVERT: C 99 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8388 (mmm160) REVERT: C 110 ASN cc_start: 0.9686 (t0) cc_final: 0.9344 (p0) REVERT: C 111 ILE cc_start: 0.9512 (mm) cc_final: 0.9238 (mm) REVERT: D 34 TYR cc_start: 0.9273 (m-80) cc_final: 0.8931 (m-80) REVERT: D 56 MET cc_start: 0.9619 (tpp) cc_final: 0.9377 (tpp) REVERT: D 58 ILE cc_start: 0.9853 (mm) cc_final: 0.9612 (mm) REVERT: D 59 MET cc_start: 0.9639 (mmp) cc_final: 0.9293 (mmm) REVERT: D 64 ASN cc_start: 0.9286 (m-40) cc_final: 0.8850 (t0) REVERT: D 65 ASP cc_start: 0.9307 (t70) cc_final: 0.8928 (t70) REVERT: D 68 GLU cc_start: 0.9324 (mp0) cc_final: 0.8563 (pm20) REVERT: E 36 MET cc_start: 0.9233 (mtm) cc_final: 0.8843 (mpp) REVERT: E 39 HIS cc_start: 0.8197 (m90) cc_final: 0.7674 (m-70) REVERT: E 50 GLU cc_start: 0.9663 (mp0) cc_final: 0.9442 (mp0) REVERT: E 56 LYS cc_start: 0.9335 (pptt) cc_final: 0.9072 (pptt) REVERT: E 86 SER cc_start: 0.9609 (p) cc_final: 0.9241 (p) REVERT: E 90 MET cc_start: 0.9270 (mmp) cc_final: 0.8910 (mmp) REVERT: E 94 GLU cc_start: 0.8929 (mp0) cc_final: 0.8565 (mp0) REVERT: E 115 LYS cc_start: 0.9461 (mppt) cc_final: 0.9105 (mmtm) REVERT: E 118 THR cc_start: 0.9084 (m) cc_final: 0.8615 (p) REVERT: E 120 MET cc_start: 0.9304 (mmp) cc_final: 0.8799 (mmm) REVERT: F 44 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8778 (mttt) REVERT: F 64 ASN cc_start: 0.9535 (t0) cc_final: 0.9158 (t0) REVERT: F 68 ASP cc_start: 0.9314 (m-30) cc_final: 0.9037 (m-30) REVERT: F 85 ASP cc_start: 0.9298 (m-30) cc_final: 0.9001 (m-30) REVERT: G 25 PHE cc_start: 0.9097 (m-80) cc_final: 0.8752 (m-10) REVERT: G 61 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9111 (mm-30) REVERT: G 94 ASN cc_start: 0.9546 (t0) cc_final: 0.9084 (m-40) REVERT: H 59 MET cc_start: 0.9693 (mmm) cc_final: 0.9241 (mmp) REVERT: H 102 GLU cc_start: 0.9294 (tp30) cc_final: 0.8976 (tp30) REVERT: S 203 ASN cc_start: 0.9735 (t0) cc_final: 0.9413 (m-40) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.1180 time to fit residues: 38.1830 Evaluate side-chains 175 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 chunk 112 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 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 = 0.3116 r_free = 0.3116 target = 0.038155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.025490 restraints weight = 141882.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.026290 restraints weight = 83342.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.026806 restraints weight = 61153.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.027125 restraints weight = 50793.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.027270 restraints weight = 45699.768| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15173 Z= 0.259 Angle : 0.708 12.905 21720 Z= 0.395 Chirality : 0.039 0.220 2447 Planarity : 0.005 0.055 1760 Dihedral : 31.462 179.608 4337 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 are not related in a simple way. whole: -0.03 (0.27), residues: 1033 helix: 0.66 (0.21), residues: 584 sheet: -1.33 (0.58), residues: 73 loop : -0.68 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 52 TYR 0.038 0.002 TYR F 88 PHE 0.020 0.002 PHE A 104 TRP 0.006 0.002 TRP S 270 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00559 (15161) covalent geometry : angle 0.66551 (21702) hydrogen bonds : bond 0.07204 ( 834) hydrogen bonds : angle 4.40265 ( 2077) metal coordination : bond 0.01330 ( 12) metal coordination : angle 8.46621 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.37 seconds wall clock time: 59 minutes 29.05 seconds (3569.05 seconds total)