Starting phenix.real_space_refine on Mon Jul 6 03:24:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqa_74562/07_2026/9zqa_74562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqa_74562/07_2026/9zqa_74562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zqa_74562/07_2026/9zqa_74562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqa_74562/07_2026/9zqa_74562.map" model { file = "/net/cci-nas-00/data/ceres_data/9zqa_74562/07_2026/9zqa_74562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqa_74562/07_2026/9zqa_74562.cif" } resolution = 3.28 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 306 5.49 5 S 40 5.16 5 C 9820 2.51 5 N 3128 2.21 5 O 3847 1.98 5 H 14563 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31704 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "C" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1627 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "D" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1700 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1695 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1372 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1413 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "K" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1489 Classifications: {'DNA': 47} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 46} Chain: "L" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 3345 Classifications: {'DNA': 106} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 105} Chain: "M" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 4874 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "P" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3583 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 222} Chain breaks: 1 Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3569 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.18 Number of scatterers: 31704 At special positions: 0 Unit cell: (142.87, 154.7, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 306 15.00 O 3847 8.00 N 3128 7.00 C 9820 6.00 H 14563 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 113 " distance=2.03 Simple disulfide: pdb=" SG CYS J 177 " - pdb=" SG CYS J 251 " distance=2.03 Simple disulfide: pdb=" SG CYS I 47 " - pdb=" SG CYS I 112 " distance=2.04 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 250 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 872.1 milliseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 25 sheets defined 44.5% alpha, 22.4% beta 153 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 46 through 73 removed outlier: 3.538A pdb=" N ASN A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.630A pdb=" N LEU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 46 through 73 removed outlier: 3.565A pdb=" N ASP B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 removed outlier: 3.607A pdb=" N LEU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'C' and resid 36 through 48 removed outlier: 3.541A pdb=" N GLN C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 47 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 83 removed outlier: 3.504A pdb=" N ASN C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.596A pdb=" N ILE C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 123 removed outlier: 4.387A pdb=" N LYS C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 54 through 83 removed outlier: 3.673A pdb=" N ASN D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.585A pdb=" N HIS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.507A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.880A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.517A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.552A pdb=" N PHE F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 115 removed outlier: 3.746A pdb=" N HIS F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 133 removed outlier: 3.755A pdb=" N ILE F 125 " --> pdb=" O MET F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'G' and resid 51 through 78 removed outlier: 4.158A pdb=" N GLU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 95 removed outlier: 3.647A pdb=" N GLN G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 32 through 44 Processing helix chain 'H' and resid 51 through 78 removed outlier: 4.069A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 78 " --> pdb=" O TYR H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 removed outlier: 3.573A pdb=" N GLN H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 185 removed outlier: 3.941A pdb=" N ALA P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 192 removed outlier: 4.183A pdb=" N GLU P 192 " --> pdb=" O GLU P 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 removed outlier: 3.540A pdb=" N THR J 108 " --> pdb=" O SER J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 185 No H-bonds generated for 'chain 'J' and resid 183 through 185' Processing helix chain 'J' and resid 217 through 220 Processing helix chain 'J' and resid 229 through 231 No H-bonds generated for 'chain 'J' and resid 229 through 231' Processing helix chain 'J' and resid 242 through 246 Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.743A pdb=" N THR I 107 " --> pdb=" O SER I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 184 No H-bonds generated for 'chain 'I' and resid 182 through 184' Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'I' and resid 241 through 245 removed outlier: 3.747A pdb=" N SER I 245 " --> pdb=" O SER I 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.785A pdb=" N ARG A 42 " --> pdb=" O ILE C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.727A pdb=" N THR A 101 " --> pdb=" O TYR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.338A pdb=" N ARG B 42 " --> pdb=" O ILE D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.787A pdb=" N THR B 101 " --> pdb=" O TYR H 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.457A pdb=" N ARG E 84 " --> pdb=" O VAL G 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.521A pdb=" N ILE E 120 " --> pdb=" O ARG G 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.868A pdb=" N ARG F 84 " --> pdb=" O VAL H 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB2, first strand: chain 'P' and resid 106 through 107 removed outlier: 3.528A pdb=" N GLY P 152 " --> pdb=" O TYR P 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.594A pdb=" N PHE J 96 " --> pdb=" O CYS J 48 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP J 95 " --> pdb=" O SER J 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 35 through 39 removed outlier: 6.698A pdb=" N MET J 36 " --> pdb=" O GLU J 130 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LYS J 132 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA J 38 " --> pdb=" O LYS J 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 109 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP J 60 " --> pdb=" O LEU J 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 35 through 39 removed outlier: 6.698A pdb=" N MET J 36 " --> pdb=" O GLU J 130 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LYS J 132 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA J 38 " --> pdb=" O LYS J 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 109 " --> pdb=" O LEU J 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 158 through 161 removed outlier: 3.505A pdb=" N THR J 233 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 165 through 167 removed outlier: 3.769A pdb=" N GLY J 204 " --> pdb=" O TRP J 191 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS J 193 " --> pdb=" O TRP J 202 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TRP J 202 " --> pdb=" O LYS J 193 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR J 195 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU J 200 " --> pdb=" O THR J 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 165 through 167 removed outlier: 4.096A pdb=" N TYR J 264 " --> pdb=" O ARG J 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 28 through 31 removed outlier: 3.709A pdb=" N PHE I 95 " --> pdb=" O CYS I 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 94 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.591A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA I 108 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP I 59 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.591A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA I 108 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR I 121 " --> pdb=" O GLN I 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 157 through 160 removed outlier: 3.515A pdb=" N THR I 232 " --> pdb=" O ASP I 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.633A pdb=" N VAL I 166 " --> pdb=" O THR I 271 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE I 188 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR I 204 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP I 190 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.633A pdb=" N VAL I 166 " --> pdb=" O THR I 271 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR I 263 " --> pdb=" O ARG I 252 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 392 hydrogen bonds 784 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14560 1.03 - 1.23: 79 1.23 - 1.42: 7812 1.42 - 1.62: 10132 1.62 - 1.81: 69 Bond restraints: 32652 Sorted by residual: bond pdb=" C3' DG M 98 " pdb=" C2' DG M 98 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.56e+00 bond pdb=" C1' DC M 30 " pdb=" N1 DC M 30 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.27e+00 bond pdb=" C1' DT M 31 " pdb=" N1 DT M 31 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.13e+00 bond pdb=" C1' DC L 37 " pdb=" N1 DC L 37 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.09e+00 bond pdb=" C3' DA M 62 " pdb=" C2' DA M 62 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.98e+00 ... (remaining 32647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.69: 59083 5.69 - 11.39: 6 11.39 - 17.08: 0 17.08 - 22.78: 0 22.78 - 28.47: 1 Bond angle restraints: 59090 Sorted by residual: angle pdb=" C SER I 118 " pdb=" N PRO I 119 " pdb=" CD PRO I 119 " ideal model delta sigma weight residual 125.00 96.53 28.47 4.10e+00 5.95e-02 4.82e+01 angle pdb=" N VAL E 118 " pdb=" CA VAL E 118 " pdb=" C VAL E 118 " ideal model delta sigma weight residual 113.53 108.72 4.81 9.80e-01 1.04e+00 2.41e+01 angle pdb=" N3 DT M 86 " pdb=" C4 DT M 86 " pdb=" O4 DT M 86 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT L 13 " pdb=" C4 DT L 13 " pdb=" O4 DT L 13 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT L 31 " pdb=" C4 DT L 31 " pdb=" O4 DT L 31 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 59085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.60: 12280 32.60 - 65.20: 1785 65.20 - 97.80: 43 97.80 - 130.40: 0 130.40 - 163.00: 3 Dihedral angle restraints: 14111 sinusoidal: 9534 harmonic: 4577 Sorted by residual: dihedral pdb=" CA SER I 118 " pdb=" C SER I 118 " pdb=" N PRO I 119 " pdb=" CA PRO I 119 " ideal model delta harmonic sigma weight residual -180.00 -148.98 -31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" C4' DG L 84 " pdb=" C3' DG L 84 " pdb=" O3' DG L 84 " pdb=" P DT L 85 " ideal model delta sinusoidal sigma weight residual 220.00 57.00 163.00 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG L 50 " pdb=" C3' DG L 50 " pdb=" O3' DG L 50 " pdb=" P DC L 51 " ideal model delta sinusoidal sigma weight residual 220.00 64.36 155.64 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 14108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2462 0.083 - 0.166: 407 0.166 - 0.249: 3 0.249 - 0.331: 1 0.331 - 0.414: 2 Chirality restraints: 2875 Sorted by residual: chirality pdb=" P DA M 4 " pdb=" OP1 DA M 4 " pdb=" OP2 DA M 4 " pdb=" O5' DA M 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" P DC K 4 " pdb=" OP1 DC K 4 " pdb=" OP2 DC K 4 " pdb=" O5' DC K 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA PRO I 119 " pdb=" N PRO I 119 " pdb=" C PRO I 119 " pdb=" CB PRO I 119 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2872 not shown) Planarity restraints: 3743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 118 " -0.131 5.00e-02 4.00e+02 2.05e-01 6.73e+01 pdb=" N PRO I 119 " 0.354 5.00e-02 4.00e+02 pdb=" CA PRO I 119 " -0.131 5.00e-02 4.00e+02 pdb=" CD PRO I 119 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 59 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" N GLU E 60 " -0.024 2.00e-02 2.50e+03 pdb=" CA GLU E 60 " 0.006 2.00e-02 2.50e+03 pdb=" H GLU E 60 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L 26 " 0.019 2.00e-02 2.50e+03 8.27e-03 1.88e+00 pdb=" N1 DC L 26 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DC L 26 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC L 26 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DC L 26 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC L 26 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC L 26 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC L 26 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC L 26 " -0.004 2.00e-02 2.50e+03 pdb=" H5 DC L 26 " 0.003 2.00e-02 2.50e+03 pdb=" H6 DC L 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 3740 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.41: 12285 2.41 - 2.96: 63891 2.96 - 3.51: 72678 3.51 - 4.05: 105725 4.05 - 4.60: 151509 Nonbonded interactions: 406088 Sorted by model distance: nonbonded pdb=" OE1 GLU E 60 " pdb=" H GLU E 60 " model vdw 1.863 2.450 nonbonded pdb=" H TYR P 201 " pdb=" HD1 TYR P 201 " model vdw 1.866 2.100 nonbonded pdb=" H VAL E 118 " pdb=" H THR E 119 " model vdw 1.875 2.100 nonbonded pdb="HH21 ARG J 55 " pdb=" HE2 TYR J 57 " model vdw 1.901 2.100 nonbonded pdb=" H LEU I 71 " pdb=" H ILE I 72 " model vdw 1.912 2.100 ... (remaining 406083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 27 through 124) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 37 through 135) selection = (chain 'F' and resid 37 through 135) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 22 through 104) } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 24 through 275) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.630 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 18093 Z= 0.424 Angle : 0.707 28.470 25736 Z= 0.570 Chirality : 0.056 0.414 2875 Planarity : 0.005 0.205 2194 Dihedral : 23.781 163.002 7550 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 0.60 % Allowed : 8.83 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.25), residues: 1344 helix: 3.24 (0.23), residues: 521 sheet: 0.83 (0.33), residues: 265 loop : -0.18 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.008 0.001 TYR I 73 PHE 0.005 0.001 PHE C 64 TRP 0.006 0.001 TRP I 201 HIS 0.004 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.42 (18089) covalent geometry : angle 0.70677 / 0.57 (25728) SS BOND : bond 0.00310 / 0.16 ( 4) SS BOND : angle 0.36123 / 0.17 ( 8) hydrogen bonds : bond 0.14048 / 9.18 ( 947) hydrogen bonds : angle 4.62711 / 3.29 ( 2362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.2072 (mttt) cc_final: 0.0115 (ttpt) REVERT: C 67 ASP cc_start: 0.9135 (t0) cc_final: 0.8720 (t0) REVERT: D 124 LYS cc_start: 0.8033 (tppt) cc_final: 0.7455 (tppt) REVERT: P 118 MET cc_start: 0.8755 (mmm) cc_final: 0.8385 (mmm) REVERT: J 25 MET cc_start: 0.8101 (mmm) cc_final: 0.7849 (mmm) REVERT: J 95 ASP cc_start: 0.8540 (p0) cc_final: 0.8231 (t0) REVERT: I 130 ILE cc_start: 0.8377 (mt) cc_final: 0.8176 (mt) outliers start: 7 outliers final: 4 residues processed: 152 average time/residue: 0.3114 time to fit residues: 67.8659 Evaluate side-chains 142 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.044908 restraints weight = 148920.077| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.42 r_work: 0.2661 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 18093 Z= 0.286 Angle : 0.641 17.300 25736 Z= 0.397 Chirality : 0.043 0.293 2875 Planarity : 0.005 0.166 2194 Dihedral : 26.845 166.231 4866 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.46 % Allowed : 7.54 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1344 helix: 2.87 (0.23), residues: 530 sheet: 0.99 (0.32), residues: 271 loop : -0.53 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 30 TYR 0.014 0.001 TYR I 73 PHE 0.013 0.001 PHE P 126 TRP 0.005 0.001 TRP P 148 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.29 (18089) covalent geometry : angle 0.64038 / 0.40 (25728) SS BOND : bond 0.00947 / 0.47 ( 4) SS BOND : angle 1.62466 / 0.76 ( 8) hydrogen bonds : bond 0.06204 / 4.24 ( 947) hydrogen bonds : angle 4.04445 / 2.88 ( 2362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.2241 (mttt) cc_final: 0.0212 (ttpt) REVERT: C 67 ASP cc_start: 0.9114 (t0) cc_final: 0.8726 (t0) REVERT: J 95 ASP cc_start: 0.8457 (p0) cc_final: 0.8236 (t0) outliers start: 17 outliers final: 14 residues processed: 144 average time/residue: 0.3042 time to fit residues: 63.6507 Evaluate side-chains 147 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 202 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 130 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.064398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.045497 restraints weight = 147568.298| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.36 r_work: 0.2681 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18093 Z= 0.180 Angle : 0.547 4.871 25736 Z= 0.359 Chirality : 0.040 0.261 2875 Planarity : 0.004 0.088 2194 Dihedral : 26.984 166.856 4866 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.02 % Favored : 95.83 % Rotamer: Outliers : 1.11 % Allowed : 8.40 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1344 helix: 3.00 (0.23), residues: 529 sheet: 0.91 (0.33), residues: 274 loop : -0.45 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.012 0.001 TYR I 73 PHE 0.009 0.001 PHE P 126 TRP 0.005 0.001 TRP P 148 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (18089) covalent geometry : angle 0.54710 / 0.36 (25728) SS BOND : bond 0.00716 / 0.36 ( 4) SS BOND : angle 1.07124 / 0.51 ( 8) hydrogen bonds : bond 0.05608 / 3.83 ( 947) hydrogen bonds : angle 3.72380 / 2.65 ( 2362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: B 11 LYS cc_start: 0.2197 (mttt) cc_final: 0.0152 (ttpt) REVERT: C 67 ASP cc_start: 0.9098 (t0) cc_final: 0.8697 (t0) outliers start: 13 outliers final: 12 residues processed: 143 average time/residue: 0.3125 time to fit residues: 64.3130 Evaluate side-chains 147 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 202 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 111 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 154 optimal weight: 0.0670 chunk 125 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.045908 restraints weight = 147362.811| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.37 r_work: 0.2695 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18093 Z= 0.155 Angle : 0.529 4.605 25736 Z= 0.347 Chirality : 0.039 0.265 2875 Planarity : 0.004 0.072 2194 Dihedral : 27.035 167.215 4866 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.94 % Favored : 95.91 % Rotamer: Outliers : 0.94 % Allowed : 8.65 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1344 helix: 3.08 (0.23), residues: 531 sheet: 0.97 (0.33), residues: 272 loop : -0.48 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.011 0.001 TYR I 73 PHE 0.007 0.001 PHE P 126 TRP 0.006 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (18089) covalent geometry : angle 0.52912 / 0.35 (25728) SS BOND : bond 0.00606 / 0.30 ( 4) SS BOND : angle 0.88693 / 0.41 ( 8) hydrogen bonds : bond 0.05086 / 3.48 ( 947) hydrogen bonds : angle 3.48306 / 2.48 ( 2362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 11 LYS cc_start: 0.2117 (mttt) cc_final: 0.0130 (ttpt) REVERT: C 67 ASP cc_start: 0.9088 (t0) cc_final: 0.8683 (t0) REVERT: J 29 MET cc_start: 0.9027 (mmm) cc_final: 0.8709 (mmm) outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.3328 time to fit residues: 70.4921 Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 202 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN P 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.045500 restraints weight = 148103.041| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.37 r_work: 0.2680 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18093 Z= 0.191 Angle : 0.545 4.664 25736 Z= 0.353 Chirality : 0.039 0.265 2875 Planarity : 0.004 0.074 2194 Dihedral : 27.087 167.564 4864 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 1.37 % Allowed : 8.91 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1344 helix: 3.02 (0.23), residues: 531 sheet: 0.95 (0.33), residues: 272 loop : -0.54 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.013 0.001 TYR I 73 PHE 0.010 0.001 PHE P 126 TRP 0.006 0.001 TRP P 148 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (18089) covalent geometry : angle 0.54510 / 0.35 (25728) SS BOND : bond 0.00651 / 0.33 ( 4) SS BOND : angle 0.95184 / 0.44 ( 8) hydrogen bonds : bond 0.05263 / 3.60 ( 947) hydrogen bonds : angle 3.46995 / 2.47 ( 2362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: B 11 LYS cc_start: 0.2182 (mttt) cc_final: 0.0187 (ttpt) REVERT: C 67 ASP cc_start: 0.9109 (t0) cc_final: 0.8714 (t0) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.3383 time to fit residues: 72.5593 Evaluate side-chains 149 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 202 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 155 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046078 restraints weight = 147286.467| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.38 r_work: 0.2701 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18093 Z= 0.136 Angle : 0.519 4.523 25736 Z= 0.340 Chirality : 0.039 0.258 2875 Planarity : 0.004 0.073 2194 Dihedral : 27.100 167.556 4864 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.21 % Rotamer: Outliers : 1.29 % Allowed : 9.25 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.24), residues: 1344 helix: 3.19 (0.23), residues: 531 sheet: 0.98 (0.33), residues: 272 loop : -0.45 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.010 0.001 TYR I 73 PHE 0.007 0.001 PHE P 176 TRP 0.005 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 (18089) covalent geometry : angle 0.51898 / 0.34 (25728) SS BOND : bond 0.00488 / 0.24 ( 4) SS BOND : angle 0.73727 / 0.34 ( 8) hydrogen bonds : bond 0.04779 / 3.27 ( 947) hydrogen bonds : angle 3.28758 / 2.34 ( 2362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: B 11 LYS cc_start: 0.2147 (mttt) cc_final: 0.0162 (ttpt) REVERT: C 67 ASP cc_start: 0.9085 (t0) cc_final: 0.8667 (t0) outliers start: 15 outliers final: 11 residues processed: 149 average time/residue: 0.3254 time to fit residues: 70.4410 Evaluate side-chains 147 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.044937 restraints weight = 147895.813| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.37 r_work: 0.2662 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18093 Z= 0.250 Angle : 0.573 5.310 25736 Z= 0.363 Chirality : 0.040 0.272 2875 Planarity : 0.004 0.078 2194 Dihedral : 27.149 167.707 4862 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 1.20 % Allowed : 9.43 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1344 helix: 3.00 (0.22), residues: 531 sheet: 0.81 (0.33), residues: 273 loop : -0.64 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.016 0.001 TYR I 73 PHE 0.011 0.001 PHE P 126 TRP 0.007 0.001 TRP P 148 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (18089) covalent geometry : angle 0.57233 / 0.36 (25728) SS BOND : bond 0.00513 / 0.26 ( 4) SS BOND : angle 1.14229 / 0.54 ( 8) hydrogen bonds : bond 0.05508 / 3.77 ( 947) hydrogen bonds : angle 3.47993 / 2.48 ( 2362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: B 11 LYS cc_start: 0.2124 (mttt) cc_final: 0.0164 (ttpt) REVERT: C 67 ASP cc_start: 0.9133 (t0) cc_final: 0.8744 (t0) outliers start: 14 outliers final: 13 residues processed: 145 average time/residue: 0.3264 time to fit residues: 68.5488 Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 202 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 137 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.045917 restraints weight = 147563.568| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.40 r_work: 0.2697 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18093 Z= 0.139 Angle : 0.524 6.151 25736 Z= 0.341 Chirality : 0.039 0.259 2875 Planarity : 0.004 0.083 2194 Dihedral : 27.172 167.752 4862 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 1.11 % Allowed : 9.77 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1344 helix: 3.15 (0.23), residues: 531 sheet: 0.91 (0.33), residues: 272 loop : -0.49 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.011 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.005 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (18089) covalent geometry : angle 0.52361 / 0.34 (25728) SS BOND : bond 0.00543 / 0.27 ( 4) SS BOND : angle 0.86877 / 0.40 ( 8) hydrogen bonds : bond 0.04812 / 3.29 ( 947) hydrogen bonds : angle 3.23999 / 2.30 ( 2362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: B 11 LYS cc_start: 0.2111 (mttt) cc_final: 0.0169 (ttpt) REVERT: B 110 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8245 (p0) REVERT: C 67 ASP cc_start: 0.9095 (t0) cc_final: 0.8696 (t0) outliers start: 13 outliers final: 10 residues processed: 146 average time/residue: 0.3426 time to fit residues: 71.6390 Evaluate side-chains 146 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 87 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 150 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045847 restraints weight = 146487.078| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.37 r_work: 0.2698 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18093 Z= 0.154 Angle : 0.530 5.868 25736 Z= 0.343 Chirality : 0.039 0.258 2875 Planarity : 0.004 0.083 2194 Dihedral : 27.153 167.539 4862 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 1.11 % Allowed : 9.94 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1344 helix: 3.18 (0.22), residues: 531 sheet: 0.91 (0.33), residues: 272 loop : -0.51 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.021 0.001 TYR P 201 PHE 0.007 0.001 PHE P 176 TRP 0.005 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (18089) covalent geometry : angle 0.52991 / 0.34 (25728) SS BOND : bond 0.00529 / 0.27 ( 4) SS BOND : angle 0.81475 / 0.37 ( 8) hydrogen bonds : bond 0.04792 / 3.28 ( 947) hydrogen bonds : angle 3.21888 / 2.28 ( 2362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: B 11 LYS cc_start: 0.2120 (mttt) cc_final: 0.0179 (ttpt) REVERT: C 67 ASP cc_start: 0.9093 (t0) cc_final: 0.8674 (t0) outliers start: 13 outliers final: 12 residues processed: 142 average time/residue: 0.3263 time to fit residues: 67.4105 Evaluate side-chains 146 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 98 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045912 restraints weight = 146865.388| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.38 r_work: 0.2694 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18093 Z= 0.158 Angle : 0.533 6.061 25736 Z= 0.344 Chirality : 0.039 0.258 2875 Planarity : 0.004 0.084 2194 Dihedral : 27.164 167.523 4862 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 1.11 % Allowed : 10.11 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1344 helix: 3.18 (0.22), residues: 532 sheet: 0.90 (0.33), residues: 272 loop : -0.53 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.012 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.005 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (18089) covalent geometry : angle 0.53285 / 0.34 (25728) SS BOND : bond 0.00541 / 0.27 ( 4) SS BOND : angle 0.81792 / 0.37 ( 8) hydrogen bonds : bond 0.04788 / 3.28 ( 947) hydrogen bonds : angle 3.20383 / 2.27 ( 2362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: B 11 LYS cc_start: 0.2127 (mttt) cc_final: 0.0186 (ttpt) REVERT: B 110 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8275 (p0) REVERT: C 67 ASP cc_start: 0.9097 (t0) cc_final: 0.8679 (t0) outliers start: 13 outliers final: 11 residues processed: 146 average time/residue: 0.3320 time to fit residues: 70.2742 Evaluate side-chains 146 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046471 restraints weight = 146713.576| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.38 r_work: 0.2708 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18093 Z= 0.135 Angle : 0.523 5.878 25736 Z= 0.339 Chirality : 0.039 0.259 2875 Planarity : 0.004 0.083 2194 Dihedral : 27.162 167.298 4862 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.03 % Allowed : 10.28 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.24), residues: 1344 helix: 3.25 (0.22), residues: 532 sheet: 0.93 (0.33), residues: 272 loop : -0.47 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.011 0.001 TYR P 201 PHE 0.007 0.001 PHE P 176 TRP 0.005 0.001 TRP P 148 HIS 0.002 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (18089) covalent geometry : angle 0.52299 / 0.34 (25728) SS BOND : bond 0.00455 / 0.23 ( 4) SS BOND : angle 0.67642 / 0.29 ( 8) hydrogen bonds : bond 0.04533 / 3.10 ( 947) hydrogen bonds : angle 3.11613 / 2.21 ( 2362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6406.46 seconds wall clock time: 109 minutes 35.30 seconds (6575.30 seconds total)