Starting phenix.real_space_refine on Sat Jul 4 09:50:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xcr_33126/07_2026/7xcr_33126.cif" } resolution = 2.57 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= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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 292 5.49 5 S 26 5.16 5 C 8789 2.51 5 N 2847 2.21 5 O 3446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15400 Number of models: 1 Model: "" Number of chains: 13 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 Time building chain proxies: 3.02, per 1000 atoms: 0.20 Number of scatterers: 15400 At special positions: 0 Unit cell: (120.96, 122.04, 130.68, 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 26 16.00 P 292 15.00 O 3446 8.00 N 2847 7.00 C 8789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 466.6 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 55.7% alpha, 5.5% beta 135 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'L' and resid 22 through 34 removed outlier: 4.048A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 4.040A pdb=" N GLN L 41 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.598A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.524A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.699A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.616A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.501A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 removed outlier: 4.028A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 55 Processing helix chain 'K' and resid 67 through 81 removed outlier: 4.338A pdb=" N MET K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 87 removed outlier: 3.596A pdb=" N GLN K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 121 through 127 Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.553A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 175 removed outlier: 3.556A pdb=" N LEU K 171 " --> pdb=" O GLY K 167 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN K 172 " --> pdb=" O GLN K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 208 removed outlier: 3.709A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 234 removed outlier: 3.524A pdb=" N ARG K 229 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 258 removed outlier: 3.506A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU K 255 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 removed outlier: 3.521A pdb=" N THR K 289 " --> pdb=" O ASP K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 286 through 289' Processing helix chain 'K' and resid 321 through 327 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.514A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 removed outlier: 3.557A pdb=" N NLE E 79 " --> pdb=" O GLN E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.572A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.595A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.564A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.621A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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 124 removed outlier: 3.575A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.524A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.728A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.624A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.199A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.155A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.062A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.758A pdb=" N THR G 101 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'K' and resid 215 through 220 removed outlier: 6.479A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.235A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 88 through 89 449 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 338 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2831 1.33 - 1.45: 5088 1.45 - 1.57: 7738 1.57 - 1.69: 582 1.69 - 1.81: 48 Bond restraints: 16287 Sorted by residual: bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.45e+01 bond pdb=" C3' DT J 89 " pdb=" C2' DT J 89 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.84e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.66e+01 bond pdb=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C1' DT I 2 " pdb=" N1 DT I 2 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 ... (remaining 16282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 22961 3.20 - 6.40: 246 6.40 - 9.60: 40 9.60 - 12.79: 5 12.79 - 15.99: 7 Bond angle restraints: 23259 Sorted by residual: angle pdb=" C GLU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 121.70 137.69 -15.99 1.80e+00 3.09e-01 7.89e+01 angle pdb=" N LEU F 37 " pdb=" CA LEU F 37 " pdb=" C LEU F 37 " ideal model delta sigma weight residual 114.75 104.75 10.00 1.26e+00 6.30e-01 6.30e+01 angle pdb=" C ARG F 67 " pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C PHE F 100 " pdb=" N GLY F 101 " pdb=" CA GLY F 101 " ideal model delta sigma weight residual 121.70 133.06 -11.36 1.80e+00 3.09e-01 3.98e+01 angle pdb=" CA PHE F 100 " pdb=" C PHE F 100 " pdb=" N GLY F 101 " ideal model delta sigma weight residual 119.07 125.58 -6.51 1.23e+00 6.61e-01 2.81e+01 ... (remaining 23254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7764 35.46 - 70.91: 1279 70.91 - 106.37: 5 106.37 - 141.83: 1 141.83 - 177.28: 2 Dihedral angle restraints: 9051 sinusoidal: 5635 harmonic: 3416 Sorted by residual: dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 116.95 63.05 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA VAL F 57 " pdb=" C VAL F 57 " pdb=" N LEU F 58 " pdb=" CA LEU F 58 " ideal model delta harmonic sigma weight residual -180.00 -138.91 -41.09 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA ASP K 32 " pdb=" C ASP K 32 " pdb=" N ALA K 33 " pdb=" CA ALA K 33 " ideal model delta harmonic sigma weight residual -180.00 -142.61 -37.39 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 9048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2112 0.073 - 0.145: 460 0.145 - 0.218: 47 0.218 - 0.290: 4 0.290 - 0.362: 3 Chirality restraints: 2626 Sorted by residual: chirality pdb=" CB ILE C 79 " pdb=" CA ILE C 79 " pdb=" CG1 ILE C 79 " pdb=" CG2 ILE C 79 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE G 79 " pdb=" CA ILE G 79 " pdb=" CG1 ILE G 79 " pdb=" CG2 ILE G 79 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB VAL F 43 " pdb=" CA VAL F 43 " pdb=" CG1 VAL F 43 " pdb=" CG2 VAL F 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2623 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 57 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C VAL F 57 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL F 57 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU F 58 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " 0.024 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE G 25 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.024 2.00e-02 2.50e+03 2.14e-02 8.02e+00 pdb=" CG PHE C 25 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.008 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2351 2.76 - 3.30: 12570 3.30 - 3.83: 28453 3.83 - 4.37: 36591 4.37 - 4.90: 52210 Nonbonded interactions: 132175 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR K 154 " pdb=" OD1 ASP K 156 " model vdw 2.302 3.040 nonbonded pdb=" O GLU K 36 " pdb=" OG1 THR K 40 " model vdw 2.341 3.040 nonbonded pdb=" NH2 ARG F 78 " pdb=" OD2 ASP F 85 " model vdw 2.342 3.120 ... (remaining 132170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.160 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 16287 Z= 0.634 Angle : 1.052 15.994 23259 Z= 0.751 Chirality : 0.059 0.362 2626 Planarity : 0.007 0.069 1940 Dihedral : 23.774 177.284 6845 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 0.90 % Allowed : 3.40 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -4.82 (0.18), residues: 1148 helix: -4.10 (0.09), residues: 665 sheet: -1.34 (0.51), residues: 80 loop : -1.44 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 45 TYR 0.031 0.003 TYR K 312 PHE 0.049 0.004 PHE G 25 TRP 0.040 0.004 TRP K 89 HIS 0.015 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.63 (16287) covalent geometry : angle 1.05239 / 0.75 (23259) hydrogen bonds : bond 0.29077 / 19.73 ( 787) hydrogen bonds : angle 9.89094 / 6.84 ( 1982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 0.301 Fit side-chains REVERT: F 53 GLU cc_start: 0.8494 (tp30) cc_final: 0.8279 (tp30) REVERT: H 54 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7999 (mt) REVERT: H 71 GLU cc_start: 0.7217 (pp20) cc_final: 0.6872 (pp20) REVERT: A 50 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 52 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7751 (mm-30) outliers start: 9 outliers final: 4 residues processed: 262 average time/residue: 0.8920 time to fit residues: 248.7406 Evaluate side-chains 175 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 60 ASN F 18 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 24 GLN G 82 HIS G 94 ASN G 110 ASN H 63 ASN K 79 ASN K 146 GLN K 324 ASN E 76 GLN E 85 GLN A 39 HIS A 68 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS C 82 HIS B 25 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135335 restraints weight = 17335.388| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.12 r_work: 0.3495 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (19 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16287 Z= 0.194 Angle : 0.812 13.064 23259 Z= 0.451 Chirality : 0.054 0.244 2626 Planarity : 0.006 0.059 1940 Dihedral : 28.982 177.817 4506 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 3.00 % Allowed : 10.41 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.22), residues: 1148 helix: -1.24 (0.17), residues: 683 sheet: -0.82 (0.57), residues: 82 loop : -0.99 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.015 0.002 TYR F 72 PHE 0.020 0.002 PHE C 25 TRP 0.022 0.003 TRP K 89 HIS 0.010 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (16287) covalent geometry : angle 0.81182 / 0.45 (23259) hydrogen bonds : bond 0.07057 / 4.68 ( 787) hydrogen bonds : angle 3.75419 / 2.51 ( 1982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: G 75 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8595 (mmtm) REVERT: H 54 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.7975 (mp) REVERT: H 71 GLU cc_start: 0.7788 (pp20) cc_final: 0.7452 (pp20) REVERT: K 113 GLN cc_start: 0.8329 (tt0) cc_final: 0.8095 (tt0) REVERT: K 212 LYS cc_start: 0.8270 (mttt) cc_final: 0.8057 (mmtm) REVERT: K 323 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6603 (mp0) REVERT: E 115 LYS cc_start: 0.8895 (mptp) cc_final: 0.8684 (mtpt) REVERT: A 50 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 79 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8432 (mppt) outliers start: 30 outliers final: 13 residues processed: 199 average time/residue: 0.8328 time to fit residues: 177.8223 Evaluate side-chains 182 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 198 MET Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain C residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 40.0000 chunk 119 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 110 ASN ** D 84 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 = 0.4090 r_free = 0.4090 target = 0.170516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136784 restraints weight = 17548.035| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.10 r_work: 0.3514 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16287 Z= 0.162 Angle : 0.702 13.025 23259 Z= 0.400 Chirality : 0.049 0.247 2626 Planarity : 0.005 0.056 1940 Dihedral : 29.274 179.263 4502 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 3.20 % Allowed : 11.61 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1148 helix: 0.08 (0.20), residues: 675 sheet: -0.45 (0.59), residues: 82 loop : -0.64 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.017 0.001 TYR F 72 PHE 0.017 0.002 PHE K 223 TRP 0.029 0.003 TRP K 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (16287) covalent geometry : angle 0.70173 / 0.40 (23259) hydrogen bonds : bond 0.05832 / 3.90 ( 787) hydrogen bonds : angle 3.33643 / 2.23 ( 1982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7749 (mt) REVERT: H 71 GLU cc_start: 0.7826 (pp20) cc_final: 0.7478 (pp20) REVERT: K 323 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6679 (mp0) REVERT: A 50 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8363 (mt-10) REVERT: D 108 LYS cc_start: 0.8478 (tttm) cc_final: 0.8277 (tttt) REVERT: C 64 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: B 79 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8436 (mppt) outliers start: 32 outliers final: 16 residues processed: 191 average time/residue: 0.8631 time to fit residues: 176.3501 Evaluate side-chains 180 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 32 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 125 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 26 optimal weight: 0.0030 chunk 85 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.9070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 84 ASN H 109 HIS K 112 GLN D 67 ASN D 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.171555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138104 restraints weight = 17617.084| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.10 r_work: 0.3534 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16287 Z= 0.143 Angle : 0.659 12.850 23259 Z= 0.376 Chirality : 0.046 0.259 2626 Planarity : 0.004 0.053 1940 Dihedral : 29.253 178.837 4502 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 3.00 % Allowed : 12.91 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1148 helix: 0.79 (0.21), residues: 671 sheet: -0.14 (0.60), residues: 82 loop : -0.34 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.010 0.001 TYR F 72 PHE 0.014 0.001 PHE K 223 TRP 0.035 0.003 TRP K 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (16287) covalent geometry : angle 0.65925 / 0.38 (23259) hydrogen bonds : bond 0.05083 / 3.38 ( 787) hydrogen bonds : angle 3.09296 / 2.08 ( 1982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7770 (mt) REVERT: H 71 GLU cc_start: 0.7792 (pp20) cc_final: 0.7469 (pp20) REVERT: K 323 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6633 (mp0) REVERT: A 50 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8399 (mt-10) REVERT: D 71 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7936 (mp0) outliers start: 30 outliers final: 18 residues processed: 188 average time/residue: 0.8423 time to fit residues: 169.8309 Evaluate side-chains 180 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS E 125 GLN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131152 restraints weight = 17417.542| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.13 r_work: 0.3444 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (26 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 16287 Z= 0.315 Angle : 0.823 12.615 23259 Z= 0.448 Chirality : 0.058 0.318 2626 Planarity : 0.007 0.059 1940 Dihedral : 29.496 176.464 4502 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % Rotamer: Outliers : 3.50 % Allowed : 13.31 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1148 helix: 0.55 (0.20), residues: 682 sheet: -0.23 (0.60), residues: 82 loop : -0.39 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 40 TYR 0.017 0.002 TYR F 88 PHE 0.019 0.003 PHE G 25 TRP 0.015 0.003 TRP K 205 HIS 0.008 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.31 (16287) covalent geometry : angle 0.82333 / 0.45 (23259) hydrogen bonds : bond 0.07607 / 5.21 ( 787) hydrogen bonds : angle 3.34468 / 2.25 ( 1982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8023 (mt) REVERT: G 75 LYS cc_start: 0.9026 (mmtp) cc_final: 0.8563 (mmtm) REVERT: H 71 GLU cc_start: 0.7881 (pp20) cc_final: 0.7558 (pp20) REVERT: A 50 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8400 (mt-10) REVERT: D 71 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: C 64 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8262 (tt0) outliers start: 35 outliers final: 24 residues processed: 181 average time/residue: 0.8390 time to fit residues: 162.5428 Evaluate side-chains 185 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134161 restraints weight = 17390.518| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.09 r_work: 0.3484 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16287 Z= 0.168 Angle : 0.720 13.412 23259 Z= 0.400 Chirality : 0.050 0.252 2626 Planarity : 0.005 0.054 1940 Dihedral : 29.513 179.095 4502 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 3.20 % Allowed : 14.01 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1148 helix: 0.88 (0.21), residues: 679 sheet: -0.02 (0.60), residues: 81 loop : -0.30 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.011 0.001 TYR D 40 PHE 0.015 0.001 PHE K 223 TRP 0.014 0.002 TRP K 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (16287) covalent geometry : angle 0.72023 / 0.40 (23259) hydrogen bonds : bond 0.05521 / 3.68 ( 787) hydrogen bonds : angle 3.14477 / 2.11 ( 1982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7946 (mt) REVERT: H 71 GLU cc_start: 0.7794 (pp20) cc_final: 0.7477 (pp20) REVERT: K 323 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6531 (mp0) REVERT: A 50 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 71 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 64 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 95 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8587 (ttmt) REVERT: B 79 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8436 (mppt) REVERT: B 95 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.6510 (mmp80) outliers start: 32 outliers final: 21 residues processed: 186 average time/residue: 0.8358 time to fit residues: 166.5719 Evaluate side-chains 184 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS K 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134531 restraints weight = 17290.095| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.08 r_work: 0.3488 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16287 Z= 0.168 Angle : 0.695 14.331 23259 Z= 0.389 Chirality : 0.049 0.376 2626 Planarity : 0.004 0.051 1940 Dihedral : 29.446 179.603 4502 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.30 % Allowed : 13.91 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1148 helix: 1.09 (0.21), residues: 679 sheet: 0.11 (0.60), residues: 81 loop : -0.22 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.020 0.001 TYR F 72 PHE 0.015 0.001 PHE K 223 TRP 0.013 0.002 TRP K 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (16287) covalent geometry : angle 0.69486 / 0.39 (23259) hydrogen bonds : bond 0.05348 / 3.57 ( 787) hydrogen bonds : angle 3.05909 / 2.06 ( 1982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7900 (mt) REVERT: G 75 LYS cc_start: 0.9046 (mmtp) cc_final: 0.8829 (mmtm) REVERT: H 71 GLU cc_start: 0.7781 (pp20) cc_final: 0.7460 (pp20) REVERT: K 323 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6553 (mp0) REVERT: A 50 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8320 (mt-10) REVERT: D 71 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: C 64 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 95 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: B 79 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8473 (mppt) outliers start: 33 outliers final: 22 residues processed: 181 average time/residue: 0.7880 time to fit residues: 152.6848 Evaluate side-chains 181 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 116 optimal weight: 10.0000 chunk 26 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.168528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134458 restraints weight = 17414.955| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.09 r_work: 0.3491 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16287 Z= 0.171 Angle : 0.690 12.706 23259 Z= 0.386 Chirality : 0.048 0.263 2626 Planarity : 0.005 0.052 1940 Dihedral : 29.443 179.128 4502 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 14.31 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1148 helix: 1.15 (0.21), residues: 679 sheet: 0.11 (0.59), residues: 81 loop : -0.16 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 92 TYR 0.011 0.001 TYR D 40 PHE 0.014 0.001 PHE K 223 TRP 0.012 0.002 TRP K 89 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (16287) covalent geometry : angle 0.69006 / 0.39 (23259) hydrogen bonds : bond 0.05304 / 3.55 ( 787) hydrogen bonds : angle 3.02168 / 2.03 ( 1982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7945 (mt) REVERT: H 54 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8498 (tt) REVERT: K 323 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6503 (mp0) REVERT: A 50 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8335 (mt-10) REVERT: D 71 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 61 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7977 (tp30) REVERT: C 64 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: C 95 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: B 79 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8469 (mppt) outliers start: 31 outliers final: 22 residues processed: 176 average time/residue: 0.8307 time to fit residues: 156.6598 Evaluate side-chains 182 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 104 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.168781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134833 restraints weight = 17355.572| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.09 r_work: 0.3497 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16287 Z= 0.153 Angle : 0.679 12.709 23259 Z= 0.382 Chirality : 0.048 0.261 2626 Planarity : 0.004 0.052 1940 Dihedral : 29.441 179.099 4502 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 14.71 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1148 helix: 1.20 (0.21), residues: 679 sheet: 0.13 (0.59), residues: 81 loop : -0.13 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.012 0.001 TYR D 40 PHE 0.014 0.001 PHE K 223 TRP 0.012 0.002 TRP K 89 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (16287) covalent geometry : angle 0.67852 / 0.38 (23259) hydrogen bonds : bond 0.05194 / 3.48 ( 787) hydrogen bonds : angle 3.01490 / 2.03 ( 1982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7907 (mt) REVERT: H 54 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8504 (tt) REVERT: K 323 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6496 (mp0) REVERT: A 50 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 71 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: C 61 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7964 (tp30) REVERT: C 64 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: C 95 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8613 (ttmt) REVERT: B 79 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8481 (mppt) outliers start: 31 outliers final: 27 residues processed: 176 average time/residue: 0.7833 time to fit residues: 147.5602 Evaluate side-chains 189 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 111 optimal weight: 40.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133240 restraints weight = 17446.846| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.11 r_work: 0.3462 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16287 Z= 0.221 Angle : 0.733 12.673 23259 Z= 0.405 Chirality : 0.052 0.271 2626 Planarity : 0.005 0.051 1940 Dihedral : 29.505 179.976 4502 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.30 % Allowed : 14.41 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1148 helix: 1.01 (0.20), residues: 682 sheet: 0.09 (0.59), residues: 81 loop : -0.17 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 92 TYR 0.010 0.002 TYR B 88 PHE 0.014 0.002 PHE K 223 TRP 0.013 0.002 TRP K 89 HIS 0.005 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (16287) covalent geometry : angle 0.73262 / 0.41 (23259) hydrogen bonds : bond 0.06071 / 4.12 ( 787) hydrogen bonds : angle 3.10995 / 2.10 ( 1982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8010 (mt) REVERT: H 54 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8559 (tt) REVERT: K 323 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6618 (mp0) REVERT: A 50 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8404 (mt-10) REVERT: D 71 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 64 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 95 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8556 (ttmt) outliers start: 33 outliers final: 25 residues processed: 178 average time/residue: 0.7993 time to fit residues: 152.6440 Evaluate side-chains 187 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS K 109 HIS E 39 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.169455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135547 restraints weight = 17324.924| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.08 r_work: 0.3498 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16287 Z= 0.136 Angle : 0.678 12.700 23259 Z= 0.382 Chirality : 0.048 0.247 2626 Planarity : 0.004 0.052 1940 Dihedral : 29.501 178.842 4502 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 2.80 % Allowed : 14.91 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1148 helix: 1.24 (0.21), residues: 679 sheet: 0.21 (0.60), residues: 81 loop : -0.11 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.016 0.001 TYR D 40 PHE 0.014 0.001 PHE K 223 TRP 0.013 0.002 TRP K 205 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (16287) covalent geometry : angle 0.67788 / 0.38 (23259) hydrogen bonds : bond 0.05002 / 3.34 ( 787) hydrogen bonds : angle 3.02576 / 2.03 ( 1982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6436.76 seconds wall clock time: 109 minutes 55.28 seconds (6595.28 seconds total)