Starting phenix.real_space_refine on Thu Aug 6 12:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syp_40889/08_2026/8syp_40889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syp_40889/08_2026/8syp_40889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8syp_40889/08_2026/8syp_40889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syp_40889/08_2026/8syp_40889.map" model { file = "/net/cci-nas-00/data/ceres_data/8syp_40889/08_2026/8syp_40889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syp_40889/08_2026/8syp_40889.cif" } resolution = 2.6 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= -0.000 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 32 5.16 5 C 8814 2.51 5 N 2809 2.21 5 O 3523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15472 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.23 Number of scatterers: 15472 At special positions: 0 Unit cell: (141.504, 125.664, 126.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 294 15.00 O 3523 8.00 N 2809 7.00 C 8814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 1.21 Conformation dependent library (CDL) restraints added in 534.4 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 22 sheets defined 47.2% alpha, 19.3% beta 134 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.918A 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 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.780A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.405A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 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 removed outlier: 3.793A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.751A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.689A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 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 76 removed outlier: 3.859A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.348A 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 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.729A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 84 through 87 removed outlier: 4.004A pdb=" N LYS M 87 " --> pdb=" O GLU M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 84 through 87' Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.877A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.577A pdb=" N ASP M 240 " --> pdb=" O GLU M 237 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 237 through 241' Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.966A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.927A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.666A 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 removed outlier: 6.524A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.216A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.903A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.212A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.513A pdb=" N GLY M 71 " --> pdb=" O TRP M 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS M 60 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP M 69 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR M 62 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU M 67 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 34 removed outlier: 4.077A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.519A pdb=" N VAL M 40 " --> pdb=" O LEU M 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 163 through 164 removed outlier: 3.637A pdb=" N VAL M 177 " --> pdb=" O ILE M 233 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE M 229 " --> pdb=" O CYS M 181 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.665A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.766A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.766A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.513A pdb=" N MET N 42 " --> pdb=" O MET N 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.757A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.65 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: 3177 1.33 - 1.46: 5535 1.46 - 1.58: 7031 1.58 - 1.70: 572 1.70 - 1.83: 52 Bond restraints: 16367 Sorted by residual: bond pdb=" O3' DT J 91 " pdb=" P DT J 92 " ideal model delta sigma weight residual 1.607 1.386 0.221 1.20e-02 6.94e+03 3.41e+02 bond pdb=" O3' DT J 92 " pdb=" P DG J 93 " ideal model delta sigma weight residual 1.607 1.392 0.215 1.20e-02 6.94e+03 3.20e+02 bond pdb=" O3' DG I 75 " pdb=" P DA I 76 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.20e-02 6.94e+03 9.29e+01 bond pdb=" O3' DA I 72 " pdb=" P DT I 73 " ideal model delta sigma weight residual 1.607 1.517 0.090 1.20e-02 6.94e+03 5.63e+01 bond pdb=" C1' DT J 92 " pdb=" N1 DT J 92 " ideal model delta sigma weight residual 1.468 1.555 -0.087 1.40e-02 5.10e+03 3.89e+01 ... (remaining 16362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.66: 23304 5.66 - 11.32: 63 11.32 - 16.99: 3 16.99 - 22.65: 2 22.65 - 28.31: 4 Bond angle restraints: 23376 Sorted by residual: angle pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " pdb=" P DG J 93 " ideal model delta sigma weight residual 119.70 91.39 28.31 1.20e+00 6.94e-01 5.57e+02 angle pdb=" C3' DT J 91 " pdb=" O3' DT J 91 " pdb=" P DT J 92 " ideal model delta sigma weight residual 119.70 147.08 -27.38 1.20e+00 6.94e-01 5.20e+02 angle pdb=" O3' DT J 92 " pdb=" P DG J 93 " pdb=" O5' DG J 93 " ideal model delta sigma weight residual 104.00 77.82 26.18 1.90e+00 2.77e-01 1.90e+02 angle pdb=" O3' DT J 91 " pdb=" P DT J 92 " pdb=" O5' DT J 92 " ideal model delta sigma weight residual 104.00 125.36 -21.36 1.90e+00 2.77e-01 1.26e+02 angle pdb=" O3' DT J 92 " pdb=" P DG J 93 " pdb=" OP2 DG J 93 " ideal model delta sigma weight residual 108.00 130.70 -22.70 3.00e+00 1.11e-01 5.72e+01 ... (remaining 23371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7439 35.46 - 70.92: 1625 70.92 - 106.37: 23 106.37 - 141.83: 1 141.83 - 177.29: 4 Dihedral angle restraints: 9092 sinusoidal: 5611 harmonic: 3481 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 37.29 -177.29 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " pdb=" O3' DC I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual -140.00 36.59 -176.59 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 53 " pdb=" C3' DG I 53 " pdb=" O3' DG I 53 " pdb=" P DC I 54 " ideal model delta sinusoidal sigma weight residual -140.00 34.03 -174.03 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2185 0.067 - 0.134: 402 0.134 - 0.201: 37 0.201 - 0.268: 8 0.268 - 0.336: 1 Chirality restraints: 2633 Sorted by residual: chirality pdb=" P DA I 76 " pdb=" OP1 DA I 76 " pdb=" OP2 DA I 76 " pdb=" O5' DA I 76 " both_signs ideal model delta sigma weight residual True 2.34 -2.00 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P DA I 72 " pdb=" OP1 DA I 72 " pdb=" OP2 DA I 72 " pdb=" O5' DA I 72 " both_signs ideal model delta sigma weight residual True 2.34 -2.10 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2630 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO N 63 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 111 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C GLU N 111 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU N 111 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP N 112 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP F 24 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.019 2.00e-02 2.50e+03 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3382 2.80 - 3.32: 12276 3.32 - 3.85: 29836 3.85 - 4.37: 35468 4.37 - 4.90: 52364 Nonbonded interactions: 133326 Sorted by model distance: nonbonded pdb=" OG1 THR A 118 " pdb=" CD ARG B 45 " model vdw 2.273 3.440 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.288 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.289 3.040 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 2.301 2.496 nonbonded pdb=" CG LYS B 77 " pdb=" NH2 ARG D 89 " model vdw 2.325 3.520 ... (remaining 133321 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 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 : 0.007 0.221 16371 Z= 0.579 Angle : 1.072 28.311 23384 Z= 0.781 Chirality : 0.053 0.336 2633 Planarity : 0.008 0.124 1931 Dihedral : 27.373 177.288 6850 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.59 % Allowed : 24.80 % Favored : 74.61 % 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: -0.62 (0.22), residues: 1175 helix: 0.09 (0.20), residues: 538 sheet: -0.13 (0.35), residues: 238 loop : -1.08 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 71 TYR 0.018 0.002 TYR N 72 PHE 0.009 0.002 PHE A 67 TRP 0.019 0.002 TRP N 199 HIS 0.007 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.58 (16367) covalent geometry : angle 1.07220 / 0.78 (23376) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 1.33386 / 0.62 ( 8) hydrogen bonds : bond 0.13295 / 8.87 ( 856) hydrogen bonds : angle 6.15185 / 4.73 ( 2156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 241 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8305 (t80) cc_final: 0.7939 (t80) REVERT: M 34 VAL cc_start: 0.9151 (t) cc_final: 0.8901 (p) REVERT: M 64 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8005 (ttp80) REVERT: M 65 GLN cc_start: 0.8614 (mt0) cc_final: 0.8248 (mt0) REVERT: N 172 SER cc_start: 0.8915 (m) cc_final: 0.8570 (p) outliers start: 6 outliers final: 5 residues processed: 245 average time/residue: 0.6971 time to fit residues: 183.7957 Evaluate side-chains 223 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN N 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.069535 restraints weight = 25607.721| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.83 r_work: 0.2664 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16371 Z= 0.187 Angle : 0.702 8.978 23384 Z= 0.393 Chirality : 0.051 0.266 2633 Planarity : 0.005 0.077 1931 Dihedral : 30.026 174.737 4567 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.05 % Allowed : 23.23 % Favored : 73.72 % 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: 0.77 (0.24), residues: 1175 helix: 1.73 (0.22), residues: 540 sheet: 0.23 (0.35), residues: 222 loop : -0.94 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 52 TYR 0.014 0.001 TYR N 72 PHE 0.008 0.001 PHE A 67 TRP 0.012 0.001 TRP N 58 HIS 0.003 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (16367) covalent geometry : angle 0.70227 / 0.39 (23376) SS BOND : bond 0.00597 / 0.30 ( 4) SS BOND : angle 1.13558 / 0.52 ( 8) hydrogen bonds : bond 0.05444 / 3.81 ( 856) hydrogen bonds : angle 3.75943 / 2.77 ( 2156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8461 (mmm) REVERT: D 65 ASP cc_start: 0.9133 (t0) cc_final: 0.8901 (t0) REVERT: E 52 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8413 (ttm-80) REVERT: E 120 MET cc_start: 0.8715 (mmm) cc_final: 0.8484 (mtt) REVERT: H 65 ASP cc_start: 0.9355 (t70) cc_final: 0.9041 (t0) REVERT: H 87 THR cc_start: 0.9169 (p) cc_final: 0.8866 (p) REVERT: H 90 GLU cc_start: 0.9102 (mp0) cc_final: 0.8677 (mp0) REVERT: M 34 VAL cc_start: 0.9249 (t) cc_final: 0.8909 (p) REVERT: M 84 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8267 (tp30) REVERT: M 240 ASP cc_start: 0.8765 (m-30) cc_final: 0.8213 (m-30) REVERT: N 95 ASP cc_start: 0.8403 (t0) cc_final: 0.8124 (t0) REVERT: N 172 SER cc_start: 0.8542 (m) cc_final: 0.8211 (p) outliers start: 31 outliers final: 13 residues processed: 233 average time/residue: 0.6655 time to fit residues: 167.4968 Evaluate side-chains 229 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.112450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.070419 restraints weight = 25905.372| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.87 r_work: 0.2683 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16371 Z= 0.145 Angle : 0.624 6.794 23384 Z= 0.358 Chirality : 0.046 0.278 2633 Planarity : 0.004 0.058 1931 Dihedral : 30.019 179.297 4562 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.66 % Allowed : 22.54 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1175 helix: 2.35 (0.22), residues: 544 sheet: 0.39 (0.36), residues: 222 loop : -0.81 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.012 0.001 TYR N 72 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP M 199 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (16367) covalent geometry : angle 0.62432 / 0.36 (23376) SS BOND : bond 0.00387 / 0.20 ( 4) SS BOND : angle 0.85010 / 0.39 ( 8) hydrogen bonds : bond 0.04778 / 3.33 ( 856) hydrogen bonds : angle 3.49422 / 2.57 ( 2156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: D 65 ASP cc_start: 0.9241 (t0) cc_final: 0.8835 (t0) REVERT: H 65 ASP cc_start: 0.9384 (t70) cc_final: 0.8966 (t0) REVERT: M 34 VAL cc_start: 0.9261 (t) cc_final: 0.8917 (p) REVERT: M 176 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7987 (ttm-80) REVERT: M 240 ASP cc_start: 0.8870 (m-30) cc_final: 0.8185 (m-30) REVERT: N 95 ASP cc_start: 0.8519 (t0) cc_final: 0.8036 (t0) REVERT: N 103 MET cc_start: 0.8625 (ttt) cc_final: 0.8160 (ttt) REVERT: N 172 SER cc_start: 0.8485 (m) cc_final: 0.8129 (p) REVERT: N 176 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7843 (ttm-80) outliers start: 27 outliers final: 12 residues processed: 236 average time/residue: 0.6225 time to fit residues: 158.9274 Evaluate side-chains 225 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 140 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.070300 restraints weight = 25856.810| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.83 r_work: 0.2753 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16371 Z= 0.151 Angle : 0.616 6.439 23384 Z= 0.351 Chirality : 0.045 0.272 2633 Planarity : 0.004 0.051 1931 Dihedral : 29.999 178.726 4562 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.15 % Allowed : 22.64 % Favored : 74.21 % 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: 1.64 (0.25), residues: 1175 helix: 2.64 (0.22), residues: 542 sheet: 0.47 (0.36), residues: 222 loop : -0.71 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.012 0.001 TYR N 72 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP M 58 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (16367) covalent geometry : angle 0.61589 / 0.35 (23376) SS BOND : bond 0.00428 / 0.22 ( 4) SS BOND : angle 0.86162 / 0.40 ( 8) hydrogen bonds : bond 0.04649 / 3.24 ( 856) hydrogen bonds : angle 3.37355 / 2.49 ( 2156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: D 65 ASP cc_start: 0.9295 (t0) cc_final: 0.8848 (t0) REVERT: E 122 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8589 (ptpt) REVERT: H 65 ASP cc_start: 0.9394 (t70) cc_final: 0.9085 (t0) REVERT: H 87 THR cc_start: 0.9169 (p) cc_final: 0.8959 (p) REVERT: H 90 GLU cc_start: 0.9083 (mp0) cc_final: 0.8671 (mp0) REVERT: M 34 VAL cc_start: 0.9224 (t) cc_final: 0.8905 (p) REVERT: M 84 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: M 240 ASP cc_start: 0.8888 (m-30) cc_final: 0.8208 (m-30) REVERT: N 25 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8407 (mm-40) REVERT: N 95 ASP cc_start: 0.8578 (t0) cc_final: 0.8102 (t0) REVERT: N 103 MET cc_start: 0.8581 (ttt) cc_final: 0.8123 (ttt) REVERT: N 172 SER cc_start: 0.8455 (m) cc_final: 0.8107 (p) outliers start: 32 outliers final: 14 residues processed: 231 average time/residue: 0.6671 time to fit residues: 166.6242 Evaluate side-chains 224 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 18 optimal weight: 0.0050 chunk 53 optimal weight: 0.0370 chunk 114 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 60 ASN E 68 GLN M 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.112940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.071168 restraints weight = 25766.436| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.84 r_work: 0.2771 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16371 Z= 0.121 Angle : 0.606 6.778 23384 Z= 0.348 Chirality : 0.045 0.275 2633 Planarity : 0.004 0.048 1931 Dihedral : 29.979 178.767 4560 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.76 % Allowed : 23.43 % Favored : 73.82 % 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: 1.73 (0.25), residues: 1175 helix: 2.72 (0.22), residues: 544 sheet: 0.52 (0.36), residues: 222 loop : -0.71 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 71 TYR 0.014 0.001 TYR N 72 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP N 58 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.12 (16367) covalent geometry : angle 0.60545 / 0.35 (23376) SS BOND : bond 0.00357 / 0.18 ( 4) SS BOND : angle 0.88429 / 0.41 ( 8) hydrogen bonds : bond 0.04446 / 3.11 ( 856) hydrogen bonds : angle 3.34367 / 2.47 ( 2156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8690 (t80) cc_final: 0.7917 (t80) REVERT: D 65 ASP cc_start: 0.9278 (t0) cc_final: 0.8923 (t0) REVERT: E 122 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8545 (ptpt) REVERT: H 65 ASP cc_start: 0.9386 (t70) cc_final: 0.8964 (t0) REVERT: H 90 GLU cc_start: 0.9093 (mp0) cc_final: 0.8758 (mp0) REVERT: M 34 VAL cc_start: 0.9327 (t) cc_final: 0.8982 (p) REVERT: M 240 ASP cc_start: 0.8890 (m-30) cc_final: 0.8178 (m-30) REVERT: N 25 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8401 (mm-40) REVERT: N 95 ASP cc_start: 0.8583 (t0) cc_final: 0.8082 (t0) REVERT: N 103 MET cc_start: 0.8568 (ttt) cc_final: 0.8194 (ttt) REVERT: N 172 SER cc_start: 0.8451 (m) cc_final: 0.8101 (p) REVERT: N 182 LYS cc_start: 0.8861 (tppp) cc_final: 0.8653 (tppp) outliers start: 28 outliers final: 14 residues processed: 227 average time/residue: 0.6494 time to fit residues: 159.2900 Evaluate side-chains 225 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.068703 restraints weight = 25679.769| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.83 r_work: 0.2650 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16371 Z= 0.216 Angle : 0.644 6.966 23384 Z= 0.360 Chirality : 0.046 0.271 2633 Planarity : 0.004 0.066 1931 Dihedral : 30.058 179.063 4560 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.95 % Allowed : 23.23 % Favored : 73.82 % 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: 1.70 (0.25), residues: 1175 helix: 2.70 (0.22), residues: 542 sheet: 0.54 (0.36), residues: 222 loop : -0.74 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 176 TYR 0.016 0.001 TYR N 72 PHE 0.010 0.001 PHE E 104 TRP 0.011 0.002 TRP M 58 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (16367) covalent geometry : angle 0.64370 / 0.36 (23376) SS BOND : bond 0.00554 / 0.28 ( 4) SS BOND : angle 0.91444 / 0.41 ( 8) hydrogen bonds : bond 0.05092 / 3.53 ( 856) hydrogen bonds : angle 3.36916 / 2.46 ( 2156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8791 (pt0) cc_final: 0.8452 (pm20) REVERT: D 39 TYR cc_start: 0.8725 (t80) cc_final: 0.7948 (t80) REVERT: D 65 ASP cc_start: 0.9298 (t0) cc_final: 0.8924 (t0) REVERT: E 122 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8534 (ptpt) REVERT: F 24 ASP cc_start: 0.7224 (t70) cc_final: 0.6041 (t70) REVERT: G 92 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8372 (mt-10) REVERT: H 65 ASP cc_start: 0.9368 (t70) cc_final: 0.8928 (t0) REVERT: H 90 GLU cc_start: 0.9015 (mp0) cc_final: 0.8475 (mp0) REVERT: M 34 VAL cc_start: 0.9304 (t) cc_final: 0.8987 (p) REVERT: M 65 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: M 84 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8251 (tp30) REVERT: M 240 ASP cc_start: 0.8905 (m-30) cc_final: 0.8218 (m-30) REVERT: N 25 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8345 (mm-40) REVERT: N 95 ASP cc_start: 0.8527 (t0) cc_final: 0.8022 (t0) REVERT: N 103 MET cc_start: 0.8664 (ttt) cc_final: 0.8248 (ttt) REVERT: N 172 SER cc_start: 0.8431 (m) cc_final: 0.7992 (p) outliers start: 30 outliers final: 16 residues processed: 224 average time/residue: 0.6732 time to fit residues: 162.6364 Evaluate side-chains 221 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070089 restraints weight = 25635.778| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.85 r_work: 0.2675 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16371 Z= 0.136 Angle : 0.635 8.974 23384 Z= 0.356 Chirality : 0.045 0.278 2633 Planarity : 0.004 0.064 1931 Dihedral : 30.047 178.749 4560 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.26 % Allowed : 23.82 % Favored : 73.92 % 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: 1.79 (0.25), residues: 1175 helix: 2.76 (0.22), residues: 542 sheet: 0.63 (0.37), residues: 222 loop : -0.71 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 23 TYR 0.011 0.001 TYR D 37 PHE 0.007 0.001 PHE A 67 TRP 0.008 0.001 TRP M 58 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (16367) covalent geometry : angle 0.63503 / 0.36 (23376) SS BOND : bond 0.00450 / 0.23 ( 4) SS BOND : angle 0.86574 / 0.41 ( 8) hydrogen bonds : bond 0.04563 / 3.17 ( 856) hydrogen bonds : angle 3.32546 / 2.43 ( 2156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8671 (t80) cc_final: 0.7891 (t80) REVERT: D 65 ASP cc_start: 0.9301 (t0) cc_final: 0.8902 (t0) REVERT: E 122 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8532 (ptpt) REVERT: G 92 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8326 (mt-10) REVERT: H 65 ASP cc_start: 0.9371 (t70) cc_final: 0.8935 (t0) REVERT: H 90 GLU cc_start: 0.9024 (mp0) cc_final: 0.8468 (mp0) REVERT: M 34 VAL cc_start: 0.9298 (t) cc_final: 0.8972 (p) REVERT: M 240 ASP cc_start: 0.8905 (m-30) cc_final: 0.8193 (m-30) REVERT: N 25 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8333 (mm-40) REVERT: N 95 ASP cc_start: 0.8547 (t0) cc_final: 0.8064 (t0) REVERT: N 103 MET cc_start: 0.8601 (ttt) cc_final: 0.8184 (ttt) REVERT: N 172 SER cc_start: 0.8272 (m) cc_final: 0.7943 (p) outliers start: 23 outliers final: 12 residues processed: 217 average time/residue: 0.6555 time to fit residues: 153.7950 Evaluate side-chains 215 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.070221 restraints weight = 25782.885| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.86 r_work: 0.2681 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16371 Z= 0.143 Angle : 0.624 9.336 23384 Z= 0.350 Chirality : 0.044 0.275 2633 Planarity : 0.004 0.073 1931 Dihedral : 29.996 178.475 4560 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 24.70 % Favored : 73.52 % 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: 1.81 (0.25), residues: 1175 helix: 2.76 (0.22), residues: 544 sheet: 0.63 (0.36), residues: 222 loop : -0.66 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 176 TYR 0.012 0.001 TYR N 72 PHE 0.008 0.001 PHE E 67 TRP 0.007 0.001 TRP M 199 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (16367) covalent geometry : angle 0.62365 / 0.35 (23376) SS BOND : bond 0.00390 / 0.20 ( 4) SS BOND : angle 0.80353 / 0.38 ( 8) hydrogen bonds : bond 0.04462 / 3.11 ( 856) hydrogen bonds : angle 3.29858 / 2.42 ( 2156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8660 (t80) cc_final: 0.7914 (t80) REVERT: D 65 ASP cc_start: 0.9272 (t0) cc_final: 0.8756 (t0) REVERT: E 122 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8503 (ptpt) REVERT: G 76 THR cc_start: 0.9114 (p) cc_final: 0.8819 (t) REVERT: G 92 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8330 (mt-10) REVERT: H 65 ASP cc_start: 0.9348 (t70) cc_final: 0.8910 (t0) REVERT: H 90 GLU cc_start: 0.8995 (mp0) cc_final: 0.8539 (mp0) REVERT: M 34 VAL cc_start: 0.9293 (t) cc_final: 0.8971 (p) REVERT: M 65 GLN cc_start: 0.8967 (mt0) cc_final: 0.8661 (mp10) REVERT: M 84 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: M 240 ASP cc_start: 0.8886 (m-30) cc_final: 0.8189 (m-30) REVERT: N 25 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8319 (mm-40) REVERT: N 64 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8248 (tmm-80) REVERT: N 95 ASP cc_start: 0.8531 (t0) cc_final: 0.8049 (t0) REVERT: N 103 MET cc_start: 0.8529 (ttt) cc_final: 0.8083 (ttt) REVERT: N 172 SER cc_start: 0.8258 (m) cc_final: 0.7929 (p) outliers start: 18 outliers final: 11 residues processed: 213 average time/residue: 0.6667 time to fit residues: 153.1142 Evaluate side-chains 216 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.069609 restraints weight = 25727.796| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.83 r_work: 0.2670 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16371 Z= 0.172 Angle : 0.632 9.230 23384 Z= 0.353 Chirality : 0.045 0.277 2633 Planarity : 0.004 0.063 1931 Dihedral : 29.991 179.237 4560 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 24.80 % Favored : 73.23 % 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: 1.78 (0.25), residues: 1175 helix: 2.69 (0.22), residues: 546 sheet: 0.70 (0.36), residues: 222 loop : -0.68 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 176 TYR 0.014 0.001 TYR N 72 PHE 0.007 0.001 PHE E 67 TRP 0.009 0.001 TRP M 58 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (16367) covalent geometry : angle 0.63195 / 0.35 (23376) SS BOND : bond 0.00454 / 0.23 ( 4) SS BOND : angle 0.87843 / 0.40 ( 8) hydrogen bonds : bond 0.04642 / 3.23 ( 856) hydrogen bonds : angle 3.31398 / 2.43 ( 2156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.363 Fit side-chains REVERT: B 84 MET cc_start: 0.8961 (mmm) cc_final: 0.8669 (tpt) REVERT: D 39 TYR cc_start: 0.8725 (t80) cc_final: 0.7978 (t80) REVERT: D 46 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.7853 (m170) REVERT: D 65 ASP cc_start: 0.9321 (t0) cc_final: 0.8841 (t0) REVERT: E 122 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (ptpt) REVERT: G 76 THR cc_start: 0.9129 (p) cc_final: 0.8845 (t) REVERT: G 92 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8378 (mt-10) REVERT: H 65 ASP cc_start: 0.9385 (t70) cc_final: 0.8953 (t0) REVERT: H 90 GLU cc_start: 0.9026 (mp0) cc_final: 0.8442 (mp0) REVERT: M 34 VAL cc_start: 0.9322 (t) cc_final: 0.8974 (p) REVERT: M 65 GLN cc_start: 0.8949 (mt0) cc_final: 0.8643 (mp10) REVERT: M 84 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: M 240 ASP cc_start: 0.8906 (m-30) cc_final: 0.8225 (m-30) REVERT: N 25 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8342 (mm-40) REVERT: N 64 ARG cc_start: 0.8526 (ttp-170) cc_final: 0.8228 (tmm-80) REVERT: N 95 ASP cc_start: 0.8612 (t0) cc_final: 0.8158 (t0) REVERT: N 103 MET cc_start: 0.8596 (ttt) cc_final: 0.8155 (ttt) REVERT: N 172 SER cc_start: 0.8346 (m) cc_final: 0.7974 (p) outliers start: 20 outliers final: 12 residues processed: 215 average time/residue: 0.6760 time to fit residues: 156.6909 Evaluate side-chains 217 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 25 GLN N 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070046 restraints weight = 25687.116| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.86 r_work: 0.2676 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16371 Z= 0.136 Angle : 0.631 9.572 23384 Z= 0.352 Chirality : 0.044 0.279 2633 Planarity : 0.004 0.040 1931 Dihedral : 29.990 179.275 4560 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.57 % Allowed : 25.20 % Favored : 73.23 % 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: 1.84 (0.26), residues: 1175 helix: 2.73 (0.22), residues: 546 sheet: 0.72 (0.37), residues: 222 loop : -0.64 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 176 TYR 0.016 0.001 TYR M 76 PHE 0.008 0.001 PHE E 67 TRP 0.009 0.001 TRP M 58 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (16367) covalent geometry : angle 0.63105 / 0.35 (23376) SS BOND : bond 0.00399 / 0.20 ( 4) SS BOND : angle 0.82672 / 0.38 ( 8) hydrogen bonds : bond 0.04501 / 3.13 ( 856) hydrogen bonds : angle 3.30500 / 2.42 ( 2156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8945 (mmm) cc_final: 0.8648 (tpt) REVERT: D 39 TYR cc_start: 0.8688 (t80) cc_final: 0.7908 (t80) REVERT: D 46 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.7800 (m170) REVERT: D 65 ASP cc_start: 0.9296 (t0) cc_final: 0.8805 (t0) REVERT: E 122 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8533 (ptpt) REVERT: G 76 THR cc_start: 0.9109 (p) cc_final: 0.8825 (t) REVERT: G 92 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8351 (mt-10) REVERT: H 65 ASP cc_start: 0.9369 (t70) cc_final: 0.8931 (t0) REVERT: H 90 GLU cc_start: 0.9003 (mp0) cc_final: 0.8457 (mp0) REVERT: M 34 VAL cc_start: 0.9317 (t) cc_final: 0.8968 (p) REVERT: M 134 GLN cc_start: 0.8785 (pm20) cc_final: 0.8534 (pm20) REVERT: M 240 ASP cc_start: 0.8899 (m-30) cc_final: 0.8203 (m-30) REVERT: N 25 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8314 (mm-40) REVERT: N 64 ARG cc_start: 0.8542 (ttp-170) cc_final: 0.8221 (tmm-80) REVERT: N 95 ASP cc_start: 0.8593 (t0) cc_final: 0.8130 (t0) REVERT: N 103 MET cc_start: 0.8545 (ttt) cc_final: 0.8102 (ttt) REVERT: N 172 SER cc_start: 0.8307 (m) cc_final: 0.7944 (p) outliers start: 16 outliers final: 12 residues processed: 212 average time/residue: 0.7269 time to fit residues: 166.3045 Evaluate side-chains 218 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 30.0000 chunk 3 optimal weight: 0.5980 chunk 116 optimal weight: 0.0020 chunk 47 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 72 optimal weight: 50.0000 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 107 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.070488 restraints weight = 25602.344| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.83 r_work: 0.2685 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16371 Z= 0.128 Angle : 0.622 9.426 23384 Z= 0.349 Chirality : 0.044 0.279 2633 Planarity : 0.004 0.041 1931 Dihedral : 29.979 179.178 4560 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.67 % Allowed : 25.10 % Favored : 73.23 % 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: 1.85 (0.25), residues: 1175 helix: 2.75 (0.22), residues: 546 sheet: 0.73 (0.37), residues: 222 loop : -0.64 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 176 TYR 0.015 0.001 TYR M 76 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP M 58 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (16367) covalent geometry : angle 0.62218 / 0.35 (23376) SS BOND : bond 0.00370 / 0.19 ( 4) SS BOND : angle 0.82038 / 0.38 ( 8) hydrogen bonds : bond 0.04422 / 3.08 ( 856) hydrogen bonds : angle 3.29678 / 2.42 ( 2156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6014.64 seconds wall clock time: 102 minutes 42.64 seconds (6162.64 seconds total)