Starting phenix.real_space_refine on Sun Sep 13 01:59:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xcr_33126/09_2026/7xcr_33126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xcr_33126/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xcr_33126/09_2026/7xcr_33126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xcr_33126/09_2026/7xcr_33126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xcr_33126/09_2026/7xcr_33126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xcr_33126/09_2026/7xcr_33126.map" model { file = "/net/cci-nas-00/data/ceres_data/7xcr_33126/09_2026/7xcr_33126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xcr_33126/09_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): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 3.29, per 1000 atoms: 0.21 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 447.7 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: 2.41 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: 3.17 Time building geometry restraints manager: 1.64 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.550 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:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- 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= 0.635 Angle : 1.057 15.994 23259 Z= 0.757 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 1.05742 / 0.76 (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 : 0.442 Fit side-chains REVERT: F 53 GLU cc_start: 0.8494 (tp30) cc_final: 0.8278 (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 42 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7963 (mmt90) REVERT: A 50 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7947 (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: 0.9111 time to fit residues: 254.2404 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 : 0.476 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 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 = 0.169437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135580 restraints weight = 17336.264| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.14 r_work: 0.3493 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 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 = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16287 Z= 0.189 Angle : 0.818 13.043 23259 Z= 0.453 Chirality : 0.054 0.253 2626 Planarity : 0.006 0.060 1940 Dihedral : 28.925 176.611 4506 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 3.20 % Allowed : 10.11 % Favored : 86.69 % 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: -1.79 (0.22), residues: 1148 helix: -1.16 (0.18), residues: 679 sheet: -0.83 (0.57), residues: 82 loop : -0.95 (0.29), residues: 387 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 K 223 TRP 0.020 0.003 TRP K 89 HIS 0.009 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (16287) covalent geometry : angle 0.81783 / 0.45 (23259) hydrogen bonds : bond 0.06841 / 4.54 ( 787) hydrogen bonds : angle 3.71269 / 2.47 ( 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 211 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: G 75 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8604 (mmtm) REVERT: H 54 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.7969 (mp) REVERT: H 71 GLU cc_start: 0.7783 (pp20) cc_final: 0.7447 (pp20) REVERT: K 113 GLN cc_start: 0.8336 (tt0) cc_final: 0.8101 (tt0) REVERT: K 212 LYS cc_start: 0.8267 (mttt) cc_final: 0.8053 (mmtm) REVERT: K 323 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6590 (mp0) REVERT: E 115 LYS cc_start: 0.8896 (mptp) cc_final: 0.8684 (mtpt) REVERT: A 42 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8233 (mtp-110) REVERT: A 50 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8342 (mt-10) REVERT: B 79 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8439 (mppt) outliers start: 32 outliers final: 15 residues processed: 200 average time/residue: 0.8368 time to fit residues: 179.2471 Evaluate side-chains 184 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 K residue 299 LEU 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 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: 10.0000 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 110 ASN H 109 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.170239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136448 restraints weight = 17508.368| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.16 r_work: 0.3494 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16287 Z= 0.163 Angle : 0.714 12.996 23259 Z= 0.402 Chirality : 0.050 0.270 2626 Planarity : 0.005 0.055 1940 Dihedral : 29.227 178.333 4502 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 3.50 % Allowed : 11.41 % Favored : 85.09 % 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: -0.33 (0.24), residues: 1148 helix: 0.18 (0.20), residues: 677 sheet: -0.44 (0.59), residues: 82 loop : -0.64 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.016 0.001 TYR F 72 PHE 0.018 0.002 PHE C 25 TRP 0.026 0.003 TRP K 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (16287) covalent geometry : angle 0.71373 / 0.40 (23259) hydrogen bonds : bond 0.05856 / 3.92 ( 787) hydrogen bonds : angle 3.31494 / 2.22 ( 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 207 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7810 (mt) REVERT: H 71 GLU cc_start: 0.7859 (pp20) cc_final: 0.7500 (pp20) REVERT: K 101 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7280 (ttm-80) REVERT: K 323 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6656 (mp0) REVERT: A 50 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8407 (mt-10) REVERT: D 108 LYS cc_start: 0.8459 (tttm) cc_final: 0.8249 (tttt) REVERT: C 64 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: B 35 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7745 (ttm-80) REVERT: B 79 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8433 (mppt) outliers start: 35 outliers final: 17 residues processed: 191 average time/residue: 0.8251 time to fit residues: 168.4383 Evaluate side-chains 188 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 101 ARG Chi-restraints excluded: chain K residue 135 VAL 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 35 ARG Chi-restraints excluded: chain B residue 79 LYS 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: 2.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 84 ASN H 109 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133845 restraints weight = 17453.799| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.12 r_work: 0.3460 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16287 Z= 0.212 Angle : 0.750 12.733 23259 Z= 0.414 Chirality : 0.052 0.283 2626 Planarity : 0.005 0.053 1940 Dihedral : 29.312 177.202 4502 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 3.60 % Allowed : 12.21 % Favored : 84.18 % 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: 0.13 (0.25), residues: 1148 helix: 0.55 (0.20), residues: 678 sheet: -0.29 (0.60), residues: 82 loop : -0.46 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.012 0.002 TYR F 72 PHE 0.017 0.002 PHE G 25 TRP 0.033 0.003 TRP K 205 HIS 0.006 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (16287) covalent geometry : angle 0.74960 / 0.41 (23259) hydrogen bonds : bond 0.06181 / 4.17 ( 787) hydrogen bonds : angle 3.26386 / 2.19 ( 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 203 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7916 (mt) REVERT: H 71 GLU cc_start: 0.7814 (pp20) cc_final: 0.7501 (pp20) REVERT: K 101 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7347 (ttm-80) REVERT: K 323 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6682 (mp0) REVERT: A 50 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8406 (mt-10) REVERT: D 108 LYS cc_start: 0.8507 (tttm) cc_final: 0.8296 (tttt) REVERT: C 64 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: B 78 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8668 (mtp-110) outliers start: 36 outliers final: 26 residues processed: 188 average time/residue: 0.8150 time to fit residues: 164.0136 Evaluate side-chains 192 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 255 GLU 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 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 78 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 78 ARG 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: 3.9990 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 112 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 109 HIS K 112 GLN D 67 ASN D 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134342 restraints weight = 17444.476| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.09 r_work: 0.3483 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- 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 = 0.30 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 = 0.34 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: 0.8473 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16287 Z= 0.177 Angle : 0.724 12.699 23259 Z= 0.402 Chirality : 0.051 0.275 2626 Planarity : 0.005 0.053 1940 Dihedral : 29.329 177.818 4502 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 3.20 % Allowed : 13.11 % Favored : 83.68 % 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: 0.41 (0.25), residues: 1148 helix: 0.81 (0.21), residues: 678 sheet: -0.22 (0.60), residues: 82 loop : -0.40 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.011 0.001 TYR D 40 PHE 0.016 0.002 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 0.00358 / 0.18 (16287) covalent geometry : angle 0.72427 / 0.40 (23259) hydrogen bonds : bond 0.05691 / 3.81 ( 787) hydrogen bonds : angle 3.18715 / 2.15 ( 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 199 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7875 (mt) REVERT: G 64 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: H 71 GLU cc_start: 0.7796 (pp20) cc_final: 0.7471 (pp20) REVERT: K 101 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7369 (ttm-80) REVERT: K 323 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6670 (mp0) REVERT: A 50 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8386 (mt-10) REVERT: C 64 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: B 78 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8637 (mtp-110) REVERT: B 95 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.6349 (mmp80) outliers start: 32 outliers final: 22 residues processed: 185 average time/residue: 0.8397 time to fit residues: 166.0242 Evaluate side-chains 190 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 64 GLU 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 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER 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 A residue 133 GLU 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 78 ARG Chi-restraints excluded: chain B residue 95 ARG 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: 9.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 40.0000 chunk 115 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 131 optimal weight: 10.9990 chunk 106 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 110 ASN H 109 HIS D 67 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131607 restraints weight = 17328.285| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.10 r_work: 0.3438 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 16287 Z= 0.288 Angle : 0.816 12.588 23259 Z= 0.443 Chirality : 0.057 0.311 2626 Planarity : 0.006 0.051 1940 Dihedral : 29.446 176.055 4502 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 4.00 % Allowed : 12.51 % Favored : 83.48 % 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: 0.22 (0.25), residues: 1148 helix: 0.64 (0.20), residues: 682 sheet: -0.33 (0.60), residues: 82 loop : -0.44 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 40 TYR 0.014 0.002 TYR B 88 PHE 0.016 0.002 PHE K 223 TRP 0.014 0.003 TRP K 89 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.29 (16287) covalent geometry : angle 0.81624 / 0.44 (23259) hydrogen bonds : bond 0.07151 / 4.87 ( 787) hydrogen bonds : angle 3.30507 / 2.23 ( 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 203 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8040 (mt) REVERT: K 101 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7300 (ttm-80) REVERT: A 50 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8406 (mt-10) REVERT: C 64 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: B 78 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8663 (mtp-110) REVERT: B 95 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7227 (mtp180) outliers start: 40 outliers final: 28 residues processed: 186 average time/residue: 0.7933 time to fit residues: 158.6330 Evaluate side-chains 194 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 294 VAL 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 78 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 78 ARG 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: 1.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.167123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133189 restraints weight = 17240.606| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.07 r_work: 0.3465 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16287 Z= 0.211 Angle : 0.755 12.663 23259 Z= 0.416 Chirality : 0.053 0.282 2626 Planarity : 0.005 0.052 1940 Dihedral : 29.469 177.466 4502 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % Rotamer: Outliers : 3.80 % Allowed : 13.21 % Favored : 82.98 % 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: 0.39 (0.25), residues: 1148 helix: 0.78 (0.20), residues: 682 sheet: -0.17 (0.60), residues: 81 loop : -0.40 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 53 TYR 0.013 0.002 TYR D 40 PHE 0.016 0.002 PHE K 223 TRP 0.013 0.002 TRP K 89 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (16287) covalent geometry : angle 0.75544 / 0.42 (23259) hydrogen bonds : bond 0.06034 / 4.05 ( 787) hydrogen bonds : angle 3.19100 / 2.15 ( 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 201 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8001 (mt) REVERT: G 64 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8306 (tp30) REVERT: K 101 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7266 (ttm-80) REVERT: K 155 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7523 (t0) REVERT: A 50 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8390 (mt-10) REVERT: C 64 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: C 95 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8536 (ttmt) REVERT: B 78 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8646 (mtp-110) REVERT: B 79 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8422 (mppt) REVERT: B 95 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6509 (mmp80) outliers start: 38 outliers final: 28 residues processed: 185 average time/residue: 0.8137 time to fit residues: 160.9182 Evaluate side-chains 194 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 64 GLU 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 59 VAL Chi-restraints excluded: chain K residue 101 ARG 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 155 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 78 SER Chi-restraints excluded: chain D residue 123 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 78 ARG Chi-restraints excluded: chain B residue 95 ARG 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: 3.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.168305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134435 restraints weight = 17410.319| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.08 r_work: 0.3483 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.38 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: 0.8471 moved from start: 0.2787 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= 0.142 Angle : 0.719 12.755 23259 Z= 0.401 Chirality : 0.050 0.274 2626 Planarity : 0.005 0.052 1940 Dihedral : 29.452 177.622 4502 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 4.00 % Allowed : 13.31 % Favored : 82.68 % 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: 0.68 (0.26), residues: 1148 helix: 1.03 (0.21), residues: 681 sheet: -0.09 (0.60), residues: 81 loop : -0.30 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 78 TYR 0.016 0.001 TYR D 40 PHE 0.014 0.002 PHE K 223 TRP 0.012 0.002 TRP K 228 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (16287) covalent geometry : angle 0.71895 / 0.40 (23259) hydrogen bonds : bond 0.05389 / 3.60 ( 787) hydrogen bonds : angle 3.14956 / 2.12 ( 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 205 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7968 (mt) REVERT: K 101 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7263 (ttm-80) REVERT: K 323 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6467 (mp0) REVERT: E 131 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8007 (mtp180) REVERT: A 50 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 64 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: C 95 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8545 (ttmt) REVERT: B 78 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8621 (mtp-110) REVERT: B 79 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8406 (mppt) outliers start: 40 outliers final: 28 residues processed: 191 average time/residue: 0.8235 time to fit residues: 168.6923 Evaluate side-chains 195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 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 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 E residue 131 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 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 78 ARG 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: 2.9990 chunk 104 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.167178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133311 restraints weight = 17352.835| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.06 r_work: 0.3467 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 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 = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16287 Z= 0.208 Angle : 0.736 12.657 23259 Z= 0.407 Chirality : 0.052 0.285 2626 Planarity : 0.005 0.052 1940 Dihedral : 29.434 177.955 4502 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.80 % Allowed : 13.51 % Favored : 82.68 % 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: 0.66 (0.25), residues: 1148 helix: 1.00 (0.21), residues: 682 sheet: -0.04 (0.60), residues: 81 loop : -0.31 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 92 TYR 0.012 0.002 TYR D 40 PHE 0.016 0.002 PHE K 223 TRP 0.013 0.002 TRP K 89 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (16287) covalent geometry : angle 0.73607 / 0.41 (23259) hydrogen bonds : bond 0.05915 / 3.98 ( 787) hydrogen bonds : angle 3.14279 / 2.12 ( 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 200 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8001 (mt) REVERT: K 101 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7232 (ttm-80) REVERT: K 206 MET cc_start: 0.8403 (mmt) cc_final: 0.7730 (mmt) REVERT: K 323 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6516 (mp0) REVERT: E 131 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8016 (mtp180) REVERT: A 50 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8387 (mt-10) REVERT: C 64 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: C 95 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8575 (ttmt) REVERT: B 78 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8671 (mtp-110) outliers start: 38 outliers final: 28 residues processed: 184 average time/residue: 0.8363 time to fit residues: 164.4460 Evaluate side-chains 195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 73 GLU 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 E residue 131 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 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 78 ARG 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: 0.4980 chunk 132 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 111 optimal weight: 40.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.167472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133541 restraints weight = 17449.993| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.08 r_work: 0.3471 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16287 Z= 0.182 Angle : 0.725 12.645 23259 Z= 0.402 Chirality : 0.051 0.283 2626 Planarity : 0.005 0.052 1940 Dihedral : 29.438 178.124 4502 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.40 % Allowed : 14.41 % 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: 0.68 (0.25), residues: 1148 helix: 1.01 (0.21), residues: 682 sheet: -0.04 (0.60), residues: 81 loop : -0.29 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.013 0.001 TYR D 40 PHE 0.015 0.002 PHE K 223 TRP 0.013 0.002 TRP K 228 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (16287) covalent geometry : angle 0.72500 / 0.40 (23259) hydrogen bonds : bond 0.05767 / 3.88 ( 787) hydrogen bonds : angle 3.13381 / 2.11 ( 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 196 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7990 (mt) REVERT: K 101 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7233 (ttm-80) REVERT: K 206 MET cc_start: 0.8400 (mmt) cc_final: 0.7741 (mmt) REVERT: K 323 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6514 (mp0) REVERT: E 131 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8023 (mtp180) REVERT: A 50 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8392 (mt-10) REVERT: C 64 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: C 95 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8575 (ttmt) REVERT: B 78 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8654 (mtp-110) REVERT: B 79 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8416 (mppt) outliers start: 34 outliers final: 28 residues processed: 182 average time/residue: 0.8336 time to fit residues: 162.1163 Evaluate side-chains 195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 73 GLU 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 E residue 131 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 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 78 ARG 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: 4.9990 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.167978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134095 restraints weight = 17282.312| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.08 r_work: 0.3479 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16287 Z= 0.143 Angle : 0.708 12.719 23259 Z= 0.395 Chirality : 0.049 0.277 2626 Planarity : 0.005 0.052 1940 Dihedral : 29.440 178.279 4502 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.20 % Allowed : 14.61 % 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: 0.78 (0.26), residues: 1148 helix: 1.10 (0.21), residues: 681 sheet: -0.02 (0.60), residues: 81 loop : -0.25 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.014 0.001 TYR D 40 PHE 0.015 0.001 PHE K 223 TRP 0.013 0.002 TRP K 228 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (16287) covalent geometry : angle 0.70753 / 0.40 (23259) hydrogen bonds : bond 0.05498 / 3.69 ( 787) hydrogen bonds : angle 3.11730 / 2.10 ( 1982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6443.03 seconds wall clock time: 109 minutes 55.70 seconds (6595.70 seconds total)