Starting phenix.real_space_refine on Thu Feb 5 14:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubk_42091/02_2026/8ubk_42091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubk_42091/02_2026/8ubk_42091.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ubk_42091/02_2026/8ubk_42091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubk_42091/02_2026/8ubk_42091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubk_42091/02_2026/8ubk_42091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubk_42091/02_2026/8ubk_42091.map" } 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= 0.001 sd= 0.028 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 324 5.49 5 S 35 5.16 5 C 10295 2.51 5 N 3315 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18041 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3311 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3331 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "O" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "P" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 642 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 313 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 8, 'ASN:plan1': 5, 'GLU:plan': 6, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "R" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 344 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 1, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 6, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 4.17, per 1000 atoms: 0.23 Number of scatterers: 18041 At special positions: 0 Unit cell: (138.336, 158.4, 177.408, 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 35 16.00 P 324 15.00 O 4072 8.00 N 3315 7.00 C 10295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.04 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.04 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.04 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: 1.69 Conformation dependent library (CDL) restraints added in 694.9 milliseconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 22 sheets defined 55.2% alpha, 17.5% beta 162 base pairs and 298 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.791A 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 removed outlier: 3.670A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.751A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.324A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 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: 3.570A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.229A 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 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.529A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.699A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'O' and resid 111 through 138 Processing helix chain 'O' and resid 150 through 171 Processing helix chain 'P' and resid 535 through 578 removed outlier: 3.851A pdb=" N LYS P 540 " --> pdb=" O PRO P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 584 through 605 Processing helix chain 'Q' and resid 111 through 140 removed outlier: 3.784A pdb=" N HIS Q 139 " --> pdb=" O THR Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 171 Processing helix chain 'R' and resid 538 through 578 Processing helix chain 'R' and resid 584 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.816A 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: 6.569A 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: 7.109A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.665A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.570A 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: 7.018A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 23 through 25 removed outlier: 3.766A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.287A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.287A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 removed outlier: 3.596A pdb=" N VAL M 167 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.332A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.332A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.781A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.516A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.516A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 removed outlier: 3.673A pdb=" N VAL N 167 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.623A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.833A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 413 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 298 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4809 1.34 - 1.46: 5726 1.46 - 1.58: 7780 1.58 - 1.71: 646 1.71 - 1.83: 57 Bond restraints: 19018 Sorted by residual: bond pdb=" C3' DC J 125 " pdb=" O3' DC J 125 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.54e+00 bond pdb=" C1' DT I 85 " pdb=" N1 DT I 85 " ideal model delta sigma weight residual 1.490 1.550 -0.060 3.00e-02 1.11e+03 4.01e+00 bond pdb=" CB LYS N 22 " pdb=" CG LYS N 22 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" C1' DC I 106 " pdb=" N1 DC I 106 " ideal model delta sigma weight residual 1.490 1.544 -0.054 3.00e-02 1.11e+03 3.25e+00 bond pdb=" N MET M 19 " pdb=" CA MET M 19 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 ... (remaining 19013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 25963 1.81 - 3.62: 993 3.62 - 5.42: 125 5.42 - 7.23: 19 7.23 - 9.04: 4 Bond angle restraints: 27104 Sorted by residual: angle pdb=" CA LYS N 22 " pdb=" CB LYS N 22 " pdb=" CG LYS N 22 " ideal model delta sigma weight residual 114.10 123.14 -9.04 2.00e+00 2.50e-01 2.04e+01 angle pdb=" OG1 THR N 236 " pdb=" CB THR N 236 " pdb=" CG2 THR N 236 " ideal model delta sigma weight residual 109.30 101.71 7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET P 572 " pdb=" CB MET P 572 " pdb=" CG MET P 572 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 angle pdb=" N GLU N 238 " pdb=" CA GLU N 238 " pdb=" CB GLU N 238 " ideal model delta sigma weight residual 110.22 115.48 -5.26 1.54e+00 4.22e-01 1.16e+01 angle pdb=" CB LYS N 22 " pdb=" CG LYS N 22 " pdb=" CD LYS N 22 " ideal model delta sigma weight residual 111.30 119.07 -7.77 2.30e+00 1.89e-01 1.14e+01 ... (remaining 27099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 9007 33.90 - 67.79: 1584 67.79 - 101.69: 51 101.69 - 135.58: 0 135.58 - 169.48: 4 Dihedral angle restraints: 10646 sinusoidal: 6314 harmonic: 4332 Sorted by residual: dihedral pdb=" CB CYS M 42 " pdb=" SG CYS M 42 " pdb=" SG CYS M 107 " pdb=" CB CYS M 107 " ideal model delta sinusoidal sigma weight residual 93.00 55.53 37.47 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " pdb=" P DG J 144 " ideal model delta sinusoidal sigma weight residual 220.00 50.52 169.48 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 10643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2293 0.042 - 0.084: 635 0.084 - 0.126: 128 0.126 - 0.168: 24 0.168 - 0.210: 1 Chirality restraints: 3081 Sorted by residual: chirality pdb=" CB THR N 236 " pdb=" CA THR N 236 " pdb=" OG1 THR N 236 " pdb=" CG2 THR N 236 " both_signs ideal model delta sigma weight residual False 2.55 2.76 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LYS M 212 " pdb=" N LYS M 212 " pdb=" C LYS M 212 " pdb=" CB LYS M 212 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA ASP N 100 " pdb=" N ASP N 100 " pdb=" C ASP N 100 " pdb=" CB ASP N 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 3078 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.005 2.00e-02 2.50e+03 1.96e-02 8.68e+00 pdb=" N1 DC I 30 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " 0.045 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.025 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.018 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 22 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C LYS N 22 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS N 22 " 0.017 2.00e-02 2.50e+03 pdb=" N MET N 23 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 134 " 0.006 2.00e-02 2.50e+03 1.42e-02 6.07e+00 pdb=" N9 DG J 134 " 0.003 2.00e-02 2.50e+03 pdb=" C8 DG J 134 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG J 134 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG J 134 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 134 " -0.018 2.00e-02 2.50e+03 pdb=" O6 DG J 134 " 0.017 2.00e-02 2.50e+03 pdb=" N1 DG J 134 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG J 134 " -0.035 2.00e-02 2.50e+03 pdb=" N2 DG J 134 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DG J 134 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG J 134 " -0.000 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 81 2.59 - 3.17: 13902 3.17 - 3.75: 31512 3.75 - 4.32: 43370 4.32 - 4.90: 64963 Nonbonded interactions: 153828 Sorted by model distance: nonbonded pdb=" OH TYR H 42 " pdb=" OP2 DC I 36 " model vdw 2.017 3.040 nonbonded pdb=" OG SER O 150 " pdb=" OE1 GLU O 153 " model vdw 2.046 3.040 nonbonded pdb=" OE1 GLU G 92 " pdb=" NH1 ARG N 251 " model vdw 2.111 3.120 nonbonded pdb=" O LYS O 151 " pdb=" OG1 THR O 154 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.221 3.040 ... (remaining 153823 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 40 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'O' and ((resid 109 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 or (resid 133 through 142 and (name N or name CA or \ name C or name O or name CB )) or (resid 143 through 171 and (name N or name CA \ or name C or name O or name CB )))) selection = chain 'Q' } ncs_group { reference = (chain 'P' and ((resid 537 through 569 and (name N or name CA or name C or name \ O or name CB )) or resid 570 or (resid 571 through 605 and (name N or name CA or \ name C or name O or name CB )))) selection = chain 'R' } 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.050 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.005 0.064 19022 Z= 0.207 Angle : 0.768 9.039 27112 Z= 0.447 Chirality : 0.041 0.210 3081 Planarity : 0.005 0.050 2327 Dihedral : 25.508 169.476 7840 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.87 % Allowed : 13.32 % Favored : 85.81 % 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: 2.30 (0.22), residues: 1457 helix: 2.77 (0.18), residues: 761 sheet: 0.61 (0.33), residues: 248 loop : -0.12 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 20 TYR 0.025 0.002 TYR H 42 PHE 0.013 0.001 PHE D 65 TRP 0.010 0.002 TRP N 185 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00488 (19018) covalent geometry : angle 0.76765 (27104) SS BOND : bond 0.01080 ( 4) SS BOND : angle 2.24129 ( 8) hydrogen bonds : bond 0.11066 ( 1166) hydrogen bonds : angle 4.46819 ( 3001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 280 time to evaluate : 0.536 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: O 124 ASN cc_start: 0.6466 (m-40) cc_final: 0.5131 (m110) REVERT: P 551 ASN cc_start: 0.7528 (p0) cc_final: 0.6616 (p0) outliers start: 10 outliers final: 5 residues processed: 288 average time/residue: 0.9246 time to fit residues: 286.3402 Evaluate side-chains 228 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 223 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 133 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 49 HIS F 93 GLN M 56 GLN M 210 ASN N 25 GLN N 96 ASN N 192 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.117643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.069678 restraints weight = 32832.487| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.92 r_work: 0.2778 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19022 Z= 0.247 Angle : 0.612 6.744 27112 Z= 0.354 Chirality : 0.038 0.166 3081 Planarity : 0.005 0.054 2327 Dihedral : 28.607 176.042 5192 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.68 % Allowed : 16.00 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.22), residues: 1457 helix: 2.95 (0.18), residues: 769 sheet: 0.99 (0.33), residues: 252 loop : -0.12 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 554 TYR 0.018 0.002 TYR C 57 PHE 0.010 0.002 PHE E 67 TRP 0.010 0.002 TRP N 196 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00562 (19018) covalent geometry : angle 0.61150 (27104) SS BOND : bond 0.00553 ( 4) SS BOND : angle 1.03231 ( 8) hydrogen bonds : bond 0.04505 ( 1166) hydrogen bonds : angle 3.58723 ( 3001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8380 (ptmm) REVERT: C 36 LYS cc_start: 0.9232 (mptt) cc_final: 0.8996 (mptt) REVERT: C 92 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8632 (mt-10) REVERT: D 71 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: F 85 ASP cc_start: 0.9175 (m-30) cc_final: 0.8967 (m-30) REVERT: G 73 ASN cc_start: 0.8449 (t160) cc_final: 0.7916 (t0) REVERT: G 75 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8725 (mmmm) REVERT: H 63 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8499 (t0) REVERT: H 68 ASP cc_start: 0.9124 (t0) cc_final: 0.8863 (t0) REVERT: M 222 ASP cc_start: 0.8315 (t0) cc_final: 0.7816 (t0) REVERT: N 191 ARG cc_start: 0.8629 (ptm-80) cc_final: 0.8417 (ptm-80) REVERT: N 222 ASP cc_start: 0.8078 (t0) cc_final: 0.7867 (t0) REVERT: O 118 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8787 (tpp-160) REVERT: P 556 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8480 (mtm110) outliers start: 31 outliers final: 8 residues processed: 249 average time/residue: 0.8098 time to fit residues: 218.1823 Evaluate side-chains 240 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 234 SER Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 133 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 158 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 171 optimal weight: 50.0000 chunk 126 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 47 GLN M 210 ASN N 96 ASN O 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.119242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071836 restraints weight = 33709.486| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.92 r_work: 0.2853 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19022 Z= 0.163 Angle : 0.564 9.181 27112 Z= 0.330 Chirality : 0.036 0.252 3081 Planarity : 0.004 0.061 2327 Dihedral : 28.456 176.672 5188 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.08 % Allowed : 17.04 % Favored : 80.88 % 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: 2.76 (0.22), residues: 1457 helix: 3.00 (0.18), residues: 770 sheet: 1.13 (0.34), residues: 252 loop : 0.08 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 121 TYR 0.016 0.001 TYR D 42 PHE 0.009 0.001 PHE E 67 TRP 0.006 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00360 (19018) covalent geometry : angle 0.56443 (27104) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.56643 ( 8) hydrogen bonds : bond 0.03896 ( 1166) hydrogen bonds : angle 3.39623 ( 3001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8270 (ptmm) REVERT: C 36 LYS cc_start: 0.9233 (mptt) cc_final: 0.8982 (mptt) REVERT: C 92 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8776 (mt-10) REVERT: D 71 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: F 85 ASP cc_start: 0.9188 (m-30) cc_final: 0.8967 (m-30) REVERT: G 73 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7861 (t0) REVERT: G 75 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8707 (mmmm) REVERT: G 104 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8738 (mm-40) REVERT: H 63 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8450 (t0) REVERT: H 68 ASP cc_start: 0.9132 (t0) cc_final: 0.8830 (t0) REVERT: M 222 ASP cc_start: 0.8302 (t0) cc_final: 0.7711 (t0) REVERT: N 47 ASP cc_start: 0.9335 (t0) cc_final: 0.9125 (t0) REVERT: N 191 ARG cc_start: 0.8641 (ptm-80) cc_final: 0.8393 (ptm-80) REVERT: N 222 ASP cc_start: 0.8091 (t0) cc_final: 0.7769 (t0) REVERT: O 118 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8804 (tpp-160) REVERT: P 560 ARG cc_start: 0.9216 (ptp-110) cc_final: 0.8946 (ptt-90) REVERT: P 577 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6287 (pp) outliers start: 24 outliers final: 6 residues processed: 250 average time/residue: 0.7884 time to fit residues: 213.1723 Evaluate side-chains 243 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 231 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 168 optimal weight: 40.0000 chunk 31 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN H 47 GLN M 210 ASN N 96 ASN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.118187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070242 restraints weight = 33643.962| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.90 r_work: 0.2824 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19022 Z= 0.195 Angle : 0.564 8.491 27112 Z= 0.329 Chirality : 0.036 0.145 3081 Planarity : 0.004 0.055 2327 Dihedral : 28.545 176.864 5188 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.60 % Allowed : 17.47 % Favored : 79.93 % 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: 2.80 (0.22), residues: 1457 helix: 2.99 (0.18), residues: 770 sheet: 1.21 (0.34), residues: 252 loop : 0.15 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 49 TYR 0.014 0.001 TYR D 42 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00439 (19018) covalent geometry : angle 0.56373 (27104) SS BOND : bond 0.00402 ( 4) SS BOND : angle 0.85468 ( 8) hydrogen bonds : bond 0.03963 ( 1166) hydrogen bonds : angle 3.32173 ( 3001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8237 (ptmm) REVERT: C 36 LYS cc_start: 0.9277 (mptt) cc_final: 0.9015 (mptt) REVERT: C 92 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8808 (mt-10) REVERT: D 71 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: D 79 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8553 (mtm110) REVERT: D 113 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8864 (mm-30) REVERT: F 85 ASP cc_start: 0.9230 (m-30) cc_final: 0.9024 (m-30) REVERT: G 56 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: G 73 ASN cc_start: 0.8511 (t160) cc_final: 0.7946 (t0) REVERT: G 75 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8809 (mmmm) REVERT: H 63 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8503 (t0) REVERT: H 68 ASP cc_start: 0.9214 (t0) cc_final: 0.8901 (t0) REVERT: H 86 ARG cc_start: 0.8581 (mmt-90) cc_final: 0.8335 (mmt90) REVERT: M 222 ASP cc_start: 0.8400 (t0) cc_final: 0.8081 (t0) REVERT: N 222 ASP cc_start: 0.8206 (t0) cc_final: 0.7822 (t70) REVERT: O 118 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.8807 (tpp-160) REVERT: O 120 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8519 (tm-30) REVERT: P 577 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6422 (pt) outliers start: 30 outliers final: 8 residues processed: 255 average time/residue: 0.8310 time to fit residues: 229.2711 Evaluate side-chains 249 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 15 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 163 optimal weight: 40.0000 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 73 ASN H 47 GLN M 210 ASN N 154 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.118857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071342 restraints weight = 33388.635| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.89 r_work: 0.2839 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19022 Z= 0.175 Angle : 0.567 15.097 27112 Z= 0.327 Chirality : 0.035 0.186 3081 Planarity : 0.004 0.066 2327 Dihedral : 28.486 177.126 5188 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.99 % Allowed : 18.69 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.86 (0.22), residues: 1457 helix: 3.02 (0.18), residues: 771 sheet: 1.28 (0.34), residues: 252 loop : 0.19 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 37 TYR 0.012 0.001 TYR D 42 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00392 (19018) covalent geometry : angle 0.56736 (27104) SS BOND : bond 0.00334 ( 4) SS BOND : angle 0.60882 ( 8) hydrogen bonds : bond 0.03791 ( 1166) hydrogen bonds : angle 3.26382 ( 3001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.9282 (mptt) cc_final: 0.9007 (mptt) REVERT: C 92 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8760 (mt-10) REVERT: C 95 LYS cc_start: 0.9246 (ttmt) cc_final: 0.8975 (tttm) REVERT: D 71 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: D 79 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8592 (mtm110) REVERT: F 85 ASP cc_start: 0.9160 (m-30) cc_final: 0.8948 (m-30) REVERT: G 56 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: G 73 ASN cc_start: 0.8412 (t0) cc_final: 0.7891 (t0) REVERT: G 104 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8718 (mm-40) REVERT: H 63 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8465 (t0) REVERT: H 68 ASP cc_start: 0.9180 (t0) cc_final: 0.8838 (t0) REVERT: M 222 ASP cc_start: 0.8344 (t0) cc_final: 0.8015 (t0) REVERT: N 222 ASP cc_start: 0.8183 (t0) cc_final: 0.7770 (t70) REVERT: O 118 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8812 (tpp-160) REVERT: O 120 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8582 (tm-30) REVERT: P 556 ARG cc_start: 0.8698 (mtm110) cc_final: 0.8469 (mtm110) REVERT: P 577 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6369 (pt) outliers start: 23 outliers final: 8 residues processed: 247 average time/residue: 0.8596 time to fit residues: 229.3673 Evaluate side-chains 242 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 171 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN N 96 ASN ** P 552 ASN ** 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 = 0.3825 r_free = 0.3825 target = 0.119235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071627 restraints weight = 33407.919| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.93 r_work: 0.2848 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19022 Z= 0.159 Angle : 0.562 11.374 27112 Z= 0.325 Chirality : 0.035 0.168 3081 Planarity : 0.005 0.090 2327 Dihedral : 28.474 177.193 5188 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.16 % Allowed : 19.38 % Favored : 78.46 % 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: 2.94 (0.22), residues: 1457 helix: 3.07 (0.18), residues: 771 sheet: 1.31 (0.35), residues: 252 loop : 0.24 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 37 TYR 0.013 0.001 TYR D 42 PHE 0.009 0.001 PHE E 67 TRP 0.006 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00349 (19018) covalent geometry : angle 0.56205 (27104) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.50057 ( 8) hydrogen bonds : bond 0.03654 ( 1166) hydrogen bonds : angle 3.24662 ( 3001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7924 (pttp) REVERT: C 20 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8284 (ttm170) REVERT: C 36 LYS cc_start: 0.9299 (mptt) cc_final: 0.9027 (mptt) REVERT: C 92 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8797 (mt-10) REVERT: C 95 LYS cc_start: 0.9281 (ttmt) cc_final: 0.9016 (tttm) REVERT: D 71 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: D 79 ARG cc_start: 0.8877 (mtm110) cc_final: 0.8663 (mtm110) REVERT: F 85 ASP cc_start: 0.9202 (m-30) cc_final: 0.8972 (m-30) REVERT: G 56 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: G 73 ASN cc_start: 0.8438 (t0) cc_final: 0.7917 (t0) REVERT: G 99 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8259 (mmp-170) REVERT: G 104 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8722 (mm-40) REVERT: H 63 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8504 (t0) REVERT: H 68 ASP cc_start: 0.9223 (t0) cc_final: 0.8945 (t0) REVERT: M 222 ASP cc_start: 0.8405 (t0) cc_final: 0.8071 (t0) REVERT: N 222 ASP cc_start: 0.8227 (t0) cc_final: 0.7823 (t70) REVERT: O 118 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8841 (tpp-160) REVERT: O 120 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8547 (tm-30) REVERT: P 577 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6312 (pt) outliers start: 25 outliers final: 9 residues processed: 248 average time/residue: 0.8539 time to fit residues: 229.0578 Evaluate side-chains 252 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 234 SER Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.119574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072118 restraints weight = 33461.046| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.89 r_work: 0.2862 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19022 Z= 0.156 Angle : 0.564 10.349 27112 Z= 0.326 Chirality : 0.035 0.145 3081 Planarity : 0.004 0.063 2327 Dihedral : 28.428 177.364 5188 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.99 % Allowed : 20.24 % Favored : 77.77 % 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: 3.01 (0.22), residues: 1457 helix: 3.11 (0.18), residues: 771 sheet: 1.38 (0.35), residues: 252 loop : 0.30 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 37 TYR 0.011 0.001 TYR D 42 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (19018) covalent geometry : angle 0.56388 (27104) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.51242 ( 8) hydrogen bonds : bond 0.03566 ( 1166) hydrogen bonds : angle 3.21024 ( 3001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9140 (m-40) cc_final: 0.8927 (m110) REVERT: C 15 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8370 (pttp) REVERT: C 36 LYS cc_start: 0.9298 (mptt) cc_final: 0.9016 (mptt) REVERT: C 92 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8798 (mt-10) REVERT: C 95 LYS cc_start: 0.9281 (ttmt) cc_final: 0.9020 (tttm) REVERT: D 71 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: D 79 ARG cc_start: 0.8874 (mtm110) cc_final: 0.8637 (mtm110) REVERT: D 116 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8834 (ttpt) REVERT: F 85 ASP cc_start: 0.9061 (m-30) cc_final: 0.8805 (m-30) REVERT: G 56 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: G 73 ASN cc_start: 0.8437 (t0) cc_final: 0.7921 (t0) REVERT: G 99 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8245 (mmp-170) REVERT: H 63 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8495 (t0) REVERT: H 68 ASP cc_start: 0.9171 (t0) cc_final: 0.8906 (t0) REVERT: M 37 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.7910 (ttm-80) REVERT: M 222 ASP cc_start: 0.8408 (t0) cc_final: 0.8073 (t0) REVERT: N 222 ASP cc_start: 0.8207 (t0) cc_final: 0.7785 (t70) REVERT: O 118 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8840 (tpp-160) REVERT: O 120 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8602 (tm-30) REVERT: P 577 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6211 (pt) outliers start: 23 outliers final: 12 residues processed: 248 average time/residue: 0.8493 time to fit residues: 227.2359 Evaluate side-chains 252 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Chi-restraints excluded: chain P residue 605 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 172 optimal weight: 50.0000 chunk 105 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 130 optimal weight: 0.0670 chunk 145 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 104 GLN N 96 ASN ** P 552 ASN ** 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 = 0.3814 r_free = 0.3814 target = 0.118558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.070760 restraints weight = 33352.504| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.93 r_work: 0.2830 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19022 Z= 0.188 Angle : 0.583 10.299 27112 Z= 0.334 Chirality : 0.036 0.155 3081 Planarity : 0.005 0.068 2327 Dihedral : 28.550 178.001 5188 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.99 % Allowed : 20.33 % Favored : 77.68 % 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: 2.97 (0.22), residues: 1457 helix: 3.07 (0.18), residues: 771 sheet: 1.33 (0.35), residues: 252 loop : 0.30 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 37 TYR 0.012 0.001 TYR F 88 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP M 60 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00424 (19018) covalent geometry : angle 0.58327 (27104) SS BOND : bond 0.00325 ( 4) SS BOND : angle 0.74345 ( 8) hydrogen bonds : bond 0.03803 ( 1166) hydrogen bonds : angle 3.24574 ( 3001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.9248 (mptt) cc_final: 0.8961 (mptt) REVERT: C 92 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8769 (mt-10) REVERT: C 95 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8968 (tttm) REVERT: D 42 TYR cc_start: 0.8490 (t80) cc_final: 0.8090 (m-80) REVERT: D 71 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: D 79 ARG cc_start: 0.8830 (mtm110) cc_final: 0.8552 (mtm110) REVERT: D 116 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8889 (ttpt) REVERT: F 85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8953 (m-30) REVERT: G 56 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: G 73 ASN cc_start: 0.8438 (t0) cc_final: 0.7886 (t0) REVERT: G 99 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8215 (mmp-170) REVERT: G 104 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8662 (mm-40) REVERT: H 63 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8500 (t0) REVERT: H 68 ASP cc_start: 0.9200 (t0) cc_final: 0.8889 (t0) REVERT: M 222 ASP cc_start: 0.8386 (t0) cc_final: 0.8035 (t0) REVERT: N 222 ASP cc_start: 0.8203 (t0) cc_final: 0.7770 (t70) REVERT: O 118 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8881 (tpp-160) REVERT: O 149 MET cc_start: 0.6943 (tmm) cc_final: 0.6597 (tmm) REVERT: P 556 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8286 (ptp-110) REVERT: P 577 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6332 (pp) outliers start: 23 outliers final: 8 residues processed: 252 average time/residue: 0.7923 time to fit residues: 216.1955 Evaluate side-chains 250 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 136 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 96 ASN ** P 552 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.119050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071518 restraints weight = 33246.088| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.85 r_work: 0.2848 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19022 Z= 0.161 Angle : 0.590 10.812 27112 Z= 0.335 Chirality : 0.035 0.164 3081 Planarity : 0.005 0.071 2327 Dihedral : 28.539 178.011 5188 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 20.59 % Favored : 77.60 % 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: 2.98 (0.22), residues: 1457 helix: 3.07 (0.18), residues: 771 sheet: 1.32 (0.35), residues: 252 loop : 0.34 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 49 TYR 0.016 0.001 TYR D 42 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP M 60 HIS 0.004 0.001 HIS P 590 Details of bonding type rmsd covalent geometry : bond 0.00357 (19018) covalent geometry : angle 0.58960 (27104) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.50372 ( 8) hydrogen bonds : bond 0.03700 ( 1166) hydrogen bonds : angle 3.24174 ( 3001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.9257 (mptt) cc_final: 0.8971 (mptt) REVERT: C 56 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8865 (tt0) REVERT: C 92 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8797 (mt-10) REVERT: C 95 LYS cc_start: 0.9274 (ttmt) cc_final: 0.9016 (tttm) REVERT: D 42 TYR cc_start: 0.8567 (t80) cc_final: 0.8123 (m-80) REVERT: D 71 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: D 79 ARG cc_start: 0.8876 (mtm110) cc_final: 0.8600 (mtm110) REVERT: D 116 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8948 (ttpt) REVERT: F 85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8948 (m-30) REVERT: G 56 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: G 73 ASN cc_start: 0.8462 (t0) cc_final: 0.7910 (t0) REVERT: G 99 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8215 (mmp-170) REVERT: G 104 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8710 (mm-40) REVERT: H 63 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8514 (t0) REVERT: H 68 ASP cc_start: 0.9205 (t0) cc_final: 0.8879 (t0) REVERT: M 222 ASP cc_start: 0.8444 (t0) cc_final: 0.8101 (t0) REVERT: N 222 ASP cc_start: 0.8257 (t0) cc_final: 0.7829 (t70) REVERT: O 118 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8903 (tpp-160) REVERT: O 149 MET cc_start: 0.6892 (tmm) cc_final: 0.6531 (tmm) REVERT: P 577 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6207 (pp) REVERT: P 605 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5205 (pm20) outliers start: 21 outliers final: 9 residues processed: 245 average time/residue: 0.7467 time to fit residues: 198.0406 Evaluate side-chains 254 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Chi-restraints excluded: chain P residue 605 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 84 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 96 ASN N 96 ASN ** P 552 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.119388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071898 restraints weight = 33322.561| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.90 r_work: 0.2859 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19022 Z= 0.168 Angle : 0.587 11.148 27112 Z= 0.335 Chirality : 0.035 0.166 3081 Planarity : 0.005 0.070 2327 Dihedral : 28.467 178.379 5188 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.38 % Allowed : 21.11 % Favored : 77.51 % 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: 2.98 (0.22), residues: 1457 helix: 3.09 (0.18), residues: 767 sheet: 1.29 (0.34), residues: 252 loop : 0.35 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 49 TYR 0.011 0.001 TYR M 199 PHE 0.009 0.001 PHE E 67 TRP 0.010 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (19018) covalent geometry : angle 0.58723 (27104) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.56253 ( 8) hydrogen bonds : bond 0.03613 ( 1166) hydrogen bonds : angle 3.22703 ( 3001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.9261 (mptt) cc_final: 0.8975 (mptt) REVERT: C 92 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8788 (mt-10) REVERT: C 95 LYS cc_start: 0.9268 (ttmt) cc_final: 0.9014 (tttm) REVERT: D 42 TYR cc_start: 0.8491 (t80) cc_final: 0.8132 (m-80) REVERT: D 71 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: D 79 ARG cc_start: 0.8854 (mtm110) cc_final: 0.8601 (mtm110) REVERT: D 116 LYS cc_start: 0.9157 (ttpt) cc_final: 0.8955 (ttpt) REVERT: F 85 ASP cc_start: 0.8970 (m-30) cc_final: 0.8716 (m-30) REVERT: G 56 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: G 73 ASN cc_start: 0.8473 (t0) cc_final: 0.7928 (t0) REVERT: G 99 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8211 (mmp-170) REVERT: G 104 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8740 (mm-40) REVERT: H 63 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8496 (t0) REVERT: H 68 ASP cc_start: 0.9211 (t0) cc_final: 0.8918 (t0) REVERT: M 222 ASP cc_start: 0.8441 (t0) cc_final: 0.8104 (t0) REVERT: N 30 MET cc_start: 0.8644 (ppp) cc_final: 0.8266 (pmm) REVERT: N 222 ASP cc_start: 0.8252 (t0) cc_final: 0.7824 (t70) REVERT: O 118 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8900 (tpp-160) REVERT: O 149 MET cc_start: 0.6320 (tmm) cc_final: 0.6062 (tmm) REVERT: O 151 LYS cc_start: 0.8445 (mppt) cc_final: 0.7970 (mmtm) REVERT: P 548 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8075 (mtt-85) REVERT: P 577 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6300 (pp) outliers start: 16 outliers final: 9 residues processed: 243 average time/residue: 0.7889 time to fit residues: 207.6426 Evaluate side-chains 248 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 577 LEU Chi-restraints excluded: chain P residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 112 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 104 GLN M 96 ASN N 154 GLN ** P 552 ASN ** 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 = 0.3816 r_free = 0.3816 target = 0.118631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071104 restraints weight = 33305.397| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.93 r_work: 0.2835 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19022 Z= 0.186 Angle : 0.598 10.977 27112 Z= 0.339 Chirality : 0.036 0.171 3081 Planarity : 0.005 0.069 2327 Dihedral : 28.561 179.036 5186 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.38 % Allowed : 20.93 % Favored : 77.68 % 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: 2.89 (0.22), residues: 1457 helix: 3.00 (0.18), residues: 771 sheet: 1.26 (0.34), residues: 252 loop : 0.31 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 49 TYR 0.011 0.001 TYR F 88 PHE 0.009 0.001 PHE E 67 TRP 0.011 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00420 (19018) covalent geometry : angle 0.59760 (27104) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.59475 ( 8) hydrogen bonds : bond 0.03798 ( 1166) hydrogen bonds : angle 3.28025 ( 3001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10562.72 seconds wall clock time: 179 minutes 20.76 seconds (10760.76 seconds total)