Starting phenix.real_space_refine on Tue Apr 7 23:44:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqa_74562/04_2026/9zqa_74562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqa_74562/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9zqa_74562/04_2026/9zqa_74562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqa_74562/04_2026/9zqa_74562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqa_74562/04_2026/9zqa_74562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqa_74562/04_2026/9zqa_74562.map" } 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-2.1rc1-6017/lib/python3.9/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: 4.24, per 1000 atoms: 0.13 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: 2.29 Conformation dependent library (CDL) restraints added in 708.5 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: 5.53 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: 7.19 Time building geometry restraints manager: 3.36 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=" CB PRO I 119 " pdb=" CG PRO I 119 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.42e+00 bond pdb=" CB GLU E 60 " pdb=" CG GLU E 60 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" C3' DG L 50 " pdb=" O3' DG L 50 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" C3' DG M 97 " pdb=" O3' DG M 97 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB GLU D 70 " pdb=" CG GLU D 70 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.82e-01 ... (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=" CB GLU E 60 " pdb=" CG GLU E 60 " pdb=" CD GLU E 60 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.70e+00 3.46e-01 1.34e+01 angle pdb=" OP1 DA M 4 " pdb=" P DA M 4 " pdb=" OP2 DA M 4 " ideal model delta sigma weight residual 120.00 109.45 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA GLU E 60 " pdb=" CB GLU E 60 " pdb=" CG GLU E 60 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+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 - 0.081: 2728 0.081 - 0.162: 144 0.162 - 0.242: 0 0.242 - 0.323: 1 0.323 - 0.404: 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 2.35 -2.75 -0.40 2.00e-01 2.50e+01 4.08e+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 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.79e+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: 0.890 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: 0.160 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.003 0.092 18093 Z= 0.137 Angle : 0.587 28.470 25736 Z= 0.340 Chirality : 0.040 0.404 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 covalent geometry : bond 0.00297 (18089) covalent geometry : angle 0.58678 (25728) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.36123 ( 8) hydrogen bonds : bond 0.14048 ( 947) hydrogen bonds : angle 4.62711 ( 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 : 0.714 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: 0.3353 time to fit residues: 71.9037 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 : 0.662 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 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: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 38 ASN P 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.044274 restraints weight = 148759.854| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.37 r_work: 0.2639 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 18093 Z= 0.293 Angle : 0.610 13.610 25736 Z= 0.367 Chirality : 0.045 0.174 2875 Planarity : 0.005 0.154 2194 Dihedral : 26.701 163.134 4866 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 1.54 % Allowed : 8.05 % 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: 1.64 (0.24), residues: 1344 helix: 2.81 (0.22), residues: 529 sheet: 0.83 (0.33), residues: 265 loop : -0.52 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 30 TYR 0.017 0.002 TYR I 73 PHE 0.014 0.001 PHE P 126 TRP 0.009 0.001 TRP P 148 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00654 (18089) covalent geometry : angle 0.60991 (25728) SS BOND : bond 0.00802 ( 4) SS BOND : angle 1.15896 ( 8) hydrogen bonds : bond 0.05989 ( 947) hydrogen bonds : angle 3.83004 ( 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 152 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.2256 (mttt) cc_final: 0.0199 (ttpt) REVERT: C 67 ASP cc_start: 0.9153 (t0) cc_final: 0.8766 (t0) REVERT: J 95 ASP cc_start: 0.8354 (p0) cc_final: 0.8143 (t0) outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 0.3175 time to fit residues: 65.8688 Evaluate side-chains 146 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 130 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.045264 restraints weight = 147538.873| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.37 r_work: 0.2672 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18093 Z= 0.185 Angle : 0.557 8.791 25736 Z= 0.340 Chirality : 0.040 0.160 2875 Planarity : 0.005 0.136 2194 Dihedral : 26.612 163.778 4866 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 1.29 % Allowed : 8.91 % Favored : 89.80 % 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: 1.77 (0.24), residues: 1344 helix: 2.97 (0.23), residues: 531 sheet: 0.86 (0.33), residues: 272 loop : -0.52 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.012 0.001 TYR I 73 PHE 0.010 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 covalent geometry : bond 0.00403 (18089) covalent geometry : angle 0.55718 (25728) SS BOND : bond 0.00512 ( 4) SS BOND : angle 0.89431 ( 8) hydrogen bonds : bond 0.04802 ( 947) hydrogen bonds : angle 3.44984 ( 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 157 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: B 11 LYS cc_start: 0.2199 (mttt) cc_final: 0.0194 (ttpt) REVERT: C 67 ASP cc_start: 0.9113 (t0) cc_final: 0.8718 (t0) outliers start: 15 outliers final: 11 residues processed: 152 average time/residue: 0.3411 time to fit residues: 73.0354 Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 58 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 111 optimal weight: 4.9990 chunk 138 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045217 restraints weight = 147266.656| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.38 r_work: 0.2669 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18093 Z= 0.192 Angle : 0.556 7.264 25736 Z= 0.340 Chirality : 0.041 0.154 2875 Planarity : 0.005 0.131 2194 Dihedral : 26.591 163.917 4864 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 1.11 % Allowed : 9.34 % Favored : 89.55 % 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: 1.73 (0.24), residues: 1344 helix: 2.97 (0.23), residues: 531 sheet: 0.81 (0.33), residues: 272 loop : -0.58 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 85 TYR 0.014 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.006 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00422 (18089) covalent geometry : angle 0.55600 (25728) SS BOND : bond 0.00528 ( 4) SS BOND : angle 0.95576 ( 8) hydrogen bonds : bond 0.04744 ( 947) hydrogen bonds : angle 3.33917 ( 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 154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: B 11 LYS cc_start: 0.2233 (mttt) cc_final: 0.0238 (ttpt) REVERT: C 67 ASP cc_start: 0.9114 (t0) cc_final: 0.8727 (t0) REVERT: D 124 LYS cc_start: 0.8745 (tppt) cc_final: 0.8502 (tppt) outliers start: 13 outliers final: 12 residues processed: 150 average time/residue: 0.3119 time to fit residues: 66.9179 Evaluate side-chains 150 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 E residue 58 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.045503 restraints weight = 148096.461| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.40 r_work: 0.2679 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.004 0.034 18093 Z= 0.177 Angle : 0.548 4.342 25736 Z= 0.335 Chirality : 0.040 0.148 2875 Planarity : 0.004 0.042 2194 Dihedral : 26.567 164.312 4864 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 1.37 % Allowed : 9.51 % 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: 1.81 (0.24), residues: 1344 helix: 3.06 (0.23), residues: 531 sheet: 0.84 (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 0.012 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.006 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00386 (18089) covalent geometry : angle 0.54761 (25728) SS BOND : bond 0.00552 ( 4) SS BOND : angle 0.84099 ( 8) hydrogen bonds : bond 0.04511 ( 947) hydrogen bonds : angle 3.23038 ( 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 : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: B 11 LYS cc_start: 0.2141 (mttt) cc_final: 0.0182 (ttpt) REVERT: B 110 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8253 (p0) REVERT: C 67 ASP cc_start: 0.9105 (t0) cc_final: 0.8716 (t0) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.3157 time to fit residues: 67.3941 Evaluate side-chains 154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 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 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 J residue 157 VAL Chi-restraints excluded: chain J residue 175 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 155 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.046121 restraints weight = 146668.392| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.40 r_work: 0.2698 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1314 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= 0.156 Angle : 0.541 4.445 25736 Z= 0.332 Chirality : 0.039 0.147 2875 Planarity : 0.004 0.052 2194 Dihedral : 26.512 164.495 4864 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 1.11 % Allowed : 10.45 % Favored : 88.43 % 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: 3.17 (0.23), residues: 533 sheet: 0.88 (0.33), residues: 272 loop : -0.54 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.011 0.001 TYR I 73 PHE 0.007 0.001 PHE P 176 TRP 0.006 0.001 TRP P 148 HIS 0.002 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00338 (18089) covalent geometry : angle 0.54138 (25728) SS BOND : bond 0.00491 ( 4) SS BOND : angle 0.73951 ( 8) hydrogen bonds : bond 0.04174 ( 947) hydrogen bonds : angle 3.09369 ( 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 157 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: B 11 LYS cc_start: 0.2145 (mttt) cc_final: 0.0172 (ttpt) REVERT: B 110 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8276 (p0) REVERT: C 67 ASP cc_start: 0.9087 (t0) cc_final: 0.8668 (t0) outliers start: 13 outliers final: 11 residues processed: 151 average time/residue: 0.3041 time to fit residues: 66.3140 Evaluate side-chains 152 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN 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 J residue 175 MET 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: 5.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.045488 restraints weight = 146993.393| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.37 r_work: 0.2679 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18093 Z= 0.191 Angle : 0.553 4.496 25736 Z= 0.338 Chirality : 0.040 0.148 2875 Planarity : 0.004 0.065 2194 Dihedral : 26.545 164.853 4864 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 1.37 % Allowed : 10.97 % Favored : 87.66 % 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: 1.85 (0.24), residues: 1344 helix: 3.11 (0.23), residues: 532 sheet: 0.85 (0.33), residues: 272 loop : -0.56 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.013 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.006 0.001 TRP P 148 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00419 (18089) covalent geometry : angle 0.55316 (25728) SS BOND : bond 0.00543 ( 4) SS BOND : angle 0.88341 ( 8) hydrogen bonds : bond 0.04577 ( 947) hydrogen bonds : angle 3.16835 ( 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 154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 11 LYS cc_start: 0.2169 (mttt) cc_final: 0.0179 (ttpt) REVERT: B 110 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8324 (p0) REVERT: C 67 ASP cc_start: 0.9108 (t0) cc_final: 0.8718 (t0) REVERT: I 154 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7209 (mtt) outliers start: 16 outliers final: 13 residues processed: 148 average time/residue: 0.3085 time to fit residues: 64.6822 Evaluate side-chains 153 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 E residue 75 ILE 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 J residue 175 MET Chi-restraints excluded: chain J residue 244 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 137 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.064383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.045512 restraints weight = 147248.064| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.37 r_work: 0.2679 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18093 Z= 0.186 Angle : 0.554 5.399 25736 Z= 0.338 Chirality : 0.040 0.147 2875 Planarity : 0.004 0.069 2194 Dihedral : 26.553 165.372 4864 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.37 % Allowed : 11.31 % Favored : 87.32 % 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: 1.85 (0.24), residues: 1344 helix: 3.13 (0.23), residues: 532 sheet: 0.84 (0.33), residues: 272 loop : -0.56 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.013 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.006 0.001 TRP P 148 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00408 (18089) covalent geometry : angle 0.55429 (25728) SS BOND : bond 0.00536 ( 4) SS BOND : angle 0.86667 ( 8) hydrogen bonds : bond 0.04534 ( 947) hydrogen bonds : angle 3.14685 ( 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 153 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: B 11 LYS cc_start: 0.2130 (mttt) cc_final: 0.0160 (ttpt) REVERT: B 110 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8336 (p0) REVERT: C 67 ASP cc_start: 0.9109 (t0) cc_final: 0.8720 (t0) REVERT: F 82 ASP cc_start: 0.8691 (p0) cc_final: 0.8483 (p0) REVERT: I 154 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7201 (mtt) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.3290 time to fit residues: 68.5555 Evaluate side-chains 150 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 J residue 175 MET Chi-restraints excluded: chain J residue 244 GLU 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: 10.0000 chunk 121 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 0.0970 chunk 160 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.046364 restraints weight = 146100.493| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.38 r_work: 0.2707 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18093 Z= 0.152 Angle : 0.545 4.661 25736 Z= 0.333 Chirality : 0.039 0.145 2875 Planarity : 0.004 0.069 2194 Dihedral : 26.470 165.430 4864 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 1.20 % Allowed : 11.57 % Favored : 87.23 % 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: 3.28 (0.23), residues: 533 sheet: 0.90 (0.33), residues: 272 loop : -0.50 (0.27), residues: 539 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 0.006 0.001 PHE P 176 TRP 0.006 0.001 TRP J 265 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00330 (18089) covalent geometry : angle 0.54486 (25728) SS BOND : bond 0.00470 ( 4) SS BOND : angle 0.70756 ( 8) hydrogen bonds : bond 0.04014 ( 947) hydrogen bonds : angle 2.99312 ( 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 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: B 11 LYS cc_start: 0.2080 (mttt) cc_final: 0.0179 (ttpt) REVERT: B 110 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8291 (p0) REVERT: C 67 ASP cc_start: 0.9080 (t0) cc_final: 0.8660 (t0) REVERT: I 154 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7186 (mtt) outliers start: 14 outliers final: 10 residues processed: 145 average time/residue: 0.3004 time to fit residues: 62.6879 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 : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN 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 J residue 175 MET 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: 4.9990 chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.046184 restraints weight = 146773.962| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.40 r_work: 0.2700 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18093 Z= 0.162 Angle : 0.550 5.201 25736 Z= 0.335 Chirality : 0.039 0.146 2875 Planarity : 0.004 0.070 2194 Dihedral : 26.456 165.203 4864 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.46 % Rotamer: Outliers : 1.11 % Allowed : 11.74 % Favored : 87.15 % 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: 3.28 (0.22), residues: 533 sheet: 0.90 (0.33), residues: 272 loop : -0.49 (0.28), residues: 539 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 0.007 0.001 PHE P 176 TRP 0.006 0.001 TRP P 148 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00353 (18089) covalent geometry : angle 0.55037 (25728) SS BOND : bond 0.00471 ( 4) SS BOND : angle 0.72438 ( 8) hydrogen bonds : bond 0.04167 ( 947) hydrogen bonds : angle 3.01087 ( 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 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: B 11 LYS cc_start: 0.2114 (mttt) cc_final: 0.0285 (tttt) REVERT: B 110 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8315 (p0) REVERT: C 67 ASP cc_start: 0.9088 (t0) cc_final: 0.8670 (t0) REVERT: I 154 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7142 (mtt) outliers start: 13 outliers final: 10 residues processed: 142 average time/residue: 0.3156 time to fit residues: 64.3161 Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 110 ASN 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 J residue 175 MET 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: 1.9990 chunk 65 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 128 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.066721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047870 restraints weight = 146856.634| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.41 r_work: 0.2753 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18093 Z= 0.131 Angle : 0.541 6.302 25736 Z= 0.329 Chirality : 0.038 0.142 2875 Planarity : 0.004 0.067 2194 Dihedral : 26.313 164.665 4864 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.03 % Allowed : 11.91 % Favored : 87.06 % 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: 2.26 (0.25), residues: 1344 helix: 3.50 (0.22), residues: 533 sheet: 1.03 (0.33), residues: 272 loop : -0.37 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 85 TYR 0.008 0.001 TYR I 204 PHE 0.006 0.001 PHE P 145 TRP 0.006 0.001 TRP J 265 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00282 (18089) covalent geometry : angle 0.54109 (25728) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.52005 ( 8) hydrogen bonds : bond 0.03459 ( 947) hydrogen bonds : angle 2.80651 ( 2362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6473.84 seconds wall clock time: 110 minutes 15.49 seconds (6615.49 seconds total)