Starting phenix.real_space_refine on Thu Aug 6 14:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2m_53532/08_2026/9r2m_53532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2m_53532/08_2026/9r2m_53532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r2m_53532/08_2026/9r2m_53532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2m_53532/08_2026/9r2m_53532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r2m_53532/08_2026/9r2m_53532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2m_53532/08_2026/9r2m_53532.map" } resolution = 3.5 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= 0.006 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 286 5.49 5 S 14 5.16 5 C 9050 2.51 5 N 3043 2.21 5 O 3578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15971 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 765 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2912 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2951 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "L" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "M" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "N" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Time building chain proxies: 3.61, per 1000 atoms: 0.23 Number of scatterers: 15971 At special positions: 0 Unit cell: (121.684, 182.525, 138.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 286 15.00 O 3578 8.00 N 3043 7.00 C 9050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 587.7 milliseconds 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2914 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 41.8% alpha, 15.0% beta 125 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.662A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.520A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.682A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.362A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.526A pdb=" N LYS D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.527A pdb=" N ARG D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.537A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.527A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.644A pdb=" N GLY F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.517A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.504A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 47 through 74 removed outlier: 3.599A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.674A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.509A pdb=" N LEU H 46 " --> pdb=" O VAL H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.570A pdb=" N ILE H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 291 removed outlier: 3.807A pdb=" N ASP K 281 " --> pdb=" O CYS K 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 4.150A pdb=" N TYR L 107 " --> pdb=" O GLN L 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY L 108 " --> pdb=" O GLY L 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 104 through 108' Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 277 through 291 Processing helix chain 'M' and resid 165 through 169 removed outlier: 3.547A pdb=" N MET M 169 " --> pdb=" O SER M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.562A pdb=" N ARG M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 290 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.977A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.347A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.521A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (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: 6.968A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (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 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.290A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 3.637A pdb=" N CYS K 135 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL K 272 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE K 251 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 6.299A pdb=" N MET L 133 " --> pdb=" O ARG L 273 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 removed outlier: 3.507A pdb=" N GLY M 112 " --> pdb=" O GLN M 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 4.169A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 4.333A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 644 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4011 1.33 - 1.45: 4058 1.45 - 1.57: 8157 1.57 - 1.69: 570 1.69 - 1.81: 24 Bond restraints: 16820 Sorted by residual: bond pdb=" C3' DC I 80 " pdb=" C2' DC I 80 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.15e+00 bond pdb=" C1' DC J 78 " pdb=" N1 DC J 78 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.58e+00 bond pdb=" C3' DG J 68 " pdb=" C2' DG J 68 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.31e+00 bond pdb=" C3' DC I 44 " pdb=" C2' DC I 44 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.30e+00 bond pdb=" C3' DT J 108 " pdb=" C2' DT J 108 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.07e+00 ... (remaining 16815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 21285 0.91 - 1.81: 2132 1.81 - 2.72: 391 2.72 - 3.63: 323 3.63 - 4.53: 16 Bond angle restraints: 24147 Sorted by residual: angle pdb=" N3 DT I 47 " pdb=" C4 DT I 47 " pdb=" O4 DT I 47 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT J 29 " pdb=" C4 DT J 29 " pdb=" O4 DT J 29 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT J 46 " pdb=" C4 DT J 46 " pdb=" O4 DT J 46 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT I 128 " pdb=" C4 DT I 128 " pdb=" O4 DT I 128 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 24142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 7367 14.38 - 28.77: 660 28.77 - 43.15: 752 43.15 - 57.54: 531 57.54 - 71.92: 48 Dihedral angle restraints: 9358 sinusoidal: 4865 harmonic: 4493 Sorted by residual: dihedral pdb=" N LYS C 76 " pdb=" CA LYS C 76 " pdb=" CB LYS C 76 " pdb=" CG LYS C 76 " ideal model delta sinusoidal sigma weight residual -60.00 -113.93 53.93 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CB ARG A 84 " pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 133.72 46.28 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" N ARG A 135 " pdb=" CA ARG A 135 " pdb=" CB ARG A 135 " pdb=" CG ARG A 135 " ideal model delta sinusoidal sigma weight residual -180.00 -135.41 -44.59 3 1.50e+01 4.44e-03 8.02e+00 ... (remaining 9355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1619 0.033 - 0.066: 651 0.066 - 0.098: 153 0.098 - 0.131: 149 0.131 - 0.164: 265 Chirality restraints: 2837 Sorted by residual: chirality pdb=" C3' DA I 64 " pdb=" C4' DA I 64 " pdb=" O3' DA I 64 " pdb=" C2' DA I 64 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C3' DG J 54 " pdb=" C4' DG J 54 " pdb=" O3' DG J 54 " pdb=" C2' DG J 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" C3' DG J 123 " pdb=" C4' DG J 123 " pdb=" O3' DG J 123 " pdb=" C2' DG J 123 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2834 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 189 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO L 190 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO L 190 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 190 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 189 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.86e-01 pdb=" N PRO N 190 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO N 190 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO N 190 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 189 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.86e-01 pdb=" N PRO M 190 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO M 190 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO M 190 " -0.014 5.00e-02 4.00e+02 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1582 2.74 - 3.28: 14128 3.28 - 3.82: 27630 3.82 - 4.36: 33462 4.36 - 4.90: 49245 Nonbonded interactions: 126047 Sorted by model distance: nonbonded pdb=" N4 DC I 18 " pdb=" O4 DT J 129 " model vdw 2.201 3.120 nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.339 3.040 nonbonded pdb=" N6 DA I 60 " pdb=" O6 DG J 87 " model vdw 2.344 3.120 nonbonded pdb=" N GLU H 94 " pdb=" OE1 GLU H 94 " model vdw 2.344 3.120 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.352 3.040 ... (remaining 126042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 4.450 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 0.041 16820 Z= 0.431 Angle : 0.669 4.534 24147 Z= 0.558 Chirality : 0.060 0.164 2837 Planarity : 0.003 0.027 2185 Dihedral : 21.338 71.920 6444 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 0.43 % Allowed : 0.14 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.18), residues: 1537 helix: -1.57 (0.17), residues: 636 sheet: -1.94 (0.26), residues: 320 loop : -1.84 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 68 TYR 0.003 0.001 TYR B 99 PHE 0.002 0.000 PHE C 26 TRP 0.000 0.000 TRP K 146 HIS 0.001 0.000 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.43 (16820) covalent geometry : angle 0.66948 / 0.56 (24147) hydrogen bonds : bond 0.22812 / 14.92 ( 936) hydrogen bonds : angle 7.64638 / 5.56 ( 2360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8231 (tpt90) cc_final: 0.7839 (tpt90) REVERT: B 51 ILE cc_start: 0.8981 (mm) cc_final: 0.8677 (mm) REVERT: C 65 GLU cc_start: 0.7811 (tt0) cc_final: 0.7595 (tt0) REVERT: C 69 ASN cc_start: 0.8206 (m-40) cc_final: 0.8004 (m-40) REVERT: C 73 ASP cc_start: 0.8965 (m-30) cc_final: 0.8700 (m-30) REVERT: C 93 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7694 (mm-30) REVERT: D 58 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8637 (mttt) REVERT: D 63 MET cc_start: 0.8635 (mmm) cc_final: 0.8405 (mmm) REVERT: D 72 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7252 (mm-30) REVERT: E 61 LEU cc_start: 0.8738 (mt) cc_final: 0.8471 (mt) REVERT: E 78 ASP cc_start: 0.8246 (m-30) cc_final: 0.7907 (t0) REVERT: E 94 GLN cc_start: 0.8599 (mt0) cc_final: 0.7919 (mt0) REVERT: F 54 GLU cc_start: 0.8204 (tp30) cc_final: 0.7978 (tp30) REVERT: F 86 ASP cc_start: 0.8522 (m-30) cc_final: 0.8303 (m-30) REVERT: G 51 TYR cc_start: 0.9040 (t80) cc_final: 0.8784 (t80) REVERT: G 74 ASN cc_start: 0.8711 (m-40) cc_final: 0.8325 (m-40) REVERT: G 91 ASP cc_start: 0.8697 (t0) cc_final: 0.8456 (t70) REVERT: G 96 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8140 (mttt) REVERT: H 68 ASN cc_start: 0.8970 (m-40) cc_final: 0.8683 (m110) REVERT: M 142 PRO cc_start: 0.6318 (Cg_exo) cc_final: 0.5966 (Cg_endo) outliers start: 3 outliers final: 1 residues processed: 268 average time/residue: 0.1563 time to fit residues: 57.0912 Evaluate side-chains 204 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN G 95 ASN H 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.074408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063739 restraints weight = 76926.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065270 restraints weight = 36185.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066260 restraints weight = 21999.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066882 restraints weight = 15702.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067311 restraints weight = 12590.119| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 16820 Z= 0.285 Angle : 0.851 11.665 24147 Z= 0.465 Chirality : 0.053 0.243 2837 Planarity : 0.006 0.051 2185 Dihedral : 26.996 77.470 4757 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.74 % Allowed : 6.35 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1537 helix: 0.70 (0.20), residues: 618 sheet: -1.23 (0.27), residues: 318 loop : -1.06 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 32 TYR 0.019 0.002 TYR B 89 PHE 0.022 0.003 PHE A 79 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (16820) covalent geometry : angle 0.85142 / 0.47 (24147) hydrogen bonds : bond 0.08121 / 5.24 ( 936) hydrogen bonds : angle 4.69389 / 3.34 ( 2360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8364 (tpt90) cc_final: 0.8006 (tpt90) REVERT: C 42 GLU cc_start: 0.8069 (tp30) cc_final: 0.7759 (tp30) REVERT: C 69 ASN cc_start: 0.8304 (m-40) cc_final: 0.8037 (m-40) REVERT: C 73 ASP cc_start: 0.8878 (m-30) cc_final: 0.8454 (m-30) REVERT: D 36 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 48 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7447 (mm-40) REVERT: D 69 ASP cc_start: 0.8108 (t0) cc_final: 0.7763 (t0) REVERT: E 63 ILE cc_start: 0.9028 (mt) cc_final: 0.8662 (mt) REVERT: E 78 ASP cc_start: 0.8460 (m-30) cc_final: 0.8191 (t0) REVERT: E 82 ASP cc_start: 0.8256 (t70) cc_final: 0.8046 (t0) REVERT: E 124 ASP cc_start: 0.8787 (m-30) cc_final: 0.8555 (m-30) REVERT: F 31 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8286 (p) REVERT: F 32 LYS cc_start: 0.8995 (ttpp) cc_final: 0.8791 (tttm) REVERT: F 54 GLU cc_start: 0.7687 (tp30) cc_final: 0.7409 (tp30) REVERT: F 86 ASP cc_start: 0.8565 (m-30) cc_final: 0.8322 (m-30) REVERT: G 51 TYR cc_start: 0.9196 (t80) cc_final: 0.8824 (t80) REVERT: G 63 ILE cc_start: 0.9291 (mt) cc_final: 0.9078 (mm) REVERT: G 74 ASN cc_start: 0.8852 (m-40) cc_final: 0.8621 (m-40) REVERT: H 68 ASN cc_start: 0.9126 (m-40) cc_final: 0.8788 (m-40) REVERT: H 69 ASP cc_start: 0.8521 (t0) cc_final: 0.8314 (t0) REVERT: H 100 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8508 (mtt-85) outliers start: 19 outliers final: 12 residues processed: 221 average time/residue: 0.1228 time to fit residues: 38.3215 Evaluate side-chains 212 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 26 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 28 GLN C 85 GLN E 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.075272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064591 restraints weight = 76396.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066184 restraints weight = 35688.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067194 restraints weight = 21391.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.067836 restraints weight = 15221.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.068196 restraints weight = 12198.720| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16820 Z= 0.154 Angle : 0.573 5.752 24147 Z= 0.340 Chirality : 0.040 0.168 2837 Planarity : 0.004 0.038 2185 Dihedral : 26.921 74.280 4753 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.16 % Allowed : 10.10 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1537 helix: 1.74 (0.21), residues: 620 sheet: -0.83 (0.29), residues: 312 loop : -0.71 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.025 0.001 TYR B 89 PHE 0.008 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (16820) covalent geometry : angle 0.57345 / 0.34 (24147) hydrogen bonds : bond 0.05157 / 3.40 ( 936) hydrogen bonds : angle 4.04247 / 2.88 ( 2360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8324 (mmp) cc_final: 0.7944 (mmt) REVERT: A 130 ARG cc_start: 0.8314 (tpt90) cc_final: 0.7955 (tpt90) REVERT: C 42 GLU cc_start: 0.8088 (tp30) cc_final: 0.7780 (tp30) REVERT: C 85 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (tp-100) REVERT: D 48 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7610 (mp10) REVERT: D 63 MET cc_start: 0.8707 (mmm) cc_final: 0.8482 (mmm) REVERT: D 69 ASP cc_start: 0.8088 (t0) cc_final: 0.7768 (t0) REVERT: D 121 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8640 (tttm) REVERT: E 74 GLU cc_start: 0.8159 (tt0) cc_final: 0.7877 (tm-30) REVERT: E 78 ASP cc_start: 0.8463 (m-30) cc_final: 0.8214 (t0) REVERT: E 82 ASP cc_start: 0.8307 (t70) cc_final: 0.7903 (t0) REVERT: F 31 THR cc_start: 0.8504 (p) cc_final: 0.8262 (p) REVERT: F 54 GLU cc_start: 0.7603 (tp30) cc_final: 0.7398 (tp30) REVERT: F 86 ASP cc_start: 0.8512 (m-30) cc_final: 0.8311 (m-30) REVERT: G 74 ASN cc_start: 0.8820 (m-40) cc_final: 0.8501 (m-40) REVERT: G 91 ASP cc_start: 0.8437 (t0) cc_final: 0.8062 (t0) REVERT: H 68 ASN cc_start: 0.9075 (m-40) cc_final: 0.8730 (m-40) REVERT: H 69 ASP cc_start: 0.8563 (t0) cc_final: 0.8247 (t0) REVERT: H 106 GLU cc_start: 0.7829 (tp30) cc_final: 0.7283 (mm-30) outliers start: 15 outliers final: 8 residues processed: 220 average time/residue: 0.1491 time to fit residues: 45.6631 Evaluate side-chains 211 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN C 69 ASN H 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058008 restraints weight = 77370.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059456 restraints weight = 37248.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060363 restraints weight = 23041.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.060950 restraints weight = 16760.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061233 restraints weight = 13627.709| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 16820 Z= 0.382 Angle : 0.898 15.024 24147 Z= 0.487 Chirality : 0.053 0.253 2837 Planarity : 0.007 0.068 2185 Dihedral : 27.766 89.048 4753 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.61 % Allowed : 9.96 % Favored : 86.44 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1537 helix: 1.12 (0.20), residues: 631 sheet: -1.41 (0.28), residues: 308 loop : -1.06 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.023 0.003 TYR D 122 PHE 0.017 0.002 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.38 (16820) covalent geometry : angle 0.89786 / 0.49 (24147) hydrogen bonds : bond 0.09157 / 6.09 ( 936) hydrogen bonds : angle 5.04238 / 3.60 ( 2360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.443 Fit side-chains REVERT: A 130 ARG cc_start: 0.8338 (tpt90) cc_final: 0.8045 (tpt90) REVERT: C 42 GLU cc_start: 0.8110 (tp30) cc_final: 0.7861 (tp30) REVERT: D 48 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7898 (mp10) REVERT: D 63 MET cc_start: 0.8886 (mmm) cc_final: 0.8647 (mmm) REVERT: D 69 ASP cc_start: 0.8199 (t0) cc_final: 0.7766 (t0) REVERT: D 121 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8559 (tttm) REVERT: E 82 ASP cc_start: 0.8416 (t70) cc_final: 0.8133 (t0) REVERT: F 86 ASP cc_start: 0.8645 (m-30) cc_final: 0.8306 (m-30) REVERT: G 50 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8684 (p) REVERT: G 73 ASP cc_start: 0.8353 (m-30) cc_final: 0.8009 (m-30) REVERT: H 68 ASN cc_start: 0.9036 (m-40) cc_final: 0.8654 (m110) REVERT: H 106 GLU cc_start: 0.7763 (tp30) cc_final: 0.6745 (mm-30) outliers start: 25 outliers final: 17 residues processed: 215 average time/residue: 0.1458 time to fit residues: 43.7622 Evaluate side-chains 214 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 0.0010 chunk 33 optimal weight: 0.8980 chunk 113 optimal weight: 0.0170 chunk 146 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 126 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.070255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060341 restraints weight = 75834.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061879 restraints weight = 35425.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062825 restraints weight = 21430.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063442 restraints weight = 15423.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063842 restraints weight = 12392.854| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16820 Z= 0.150 Angle : 0.603 9.678 24147 Z= 0.352 Chirality : 0.041 0.188 2837 Planarity : 0.005 0.055 2185 Dihedral : 27.416 77.412 4753 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.16 % Allowed : 12.99 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1537 helix: 1.91 (0.21), residues: 632 sheet: -1.03 (0.29), residues: 296 loop : -0.60 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.022 0.002 TYR D 84 PHE 0.017 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (16820) covalent geometry : angle 0.60317 / 0.35 (24147) hydrogen bonds : bond 0.04653 / 3.06 ( 936) hydrogen bonds : angle 4.02968 / 2.86 ( 2360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.451 Fit side-chains REVERT: A 91 MET cc_start: 0.8319 (mmp) cc_final: 0.7994 (mmp) REVERT: A 130 ARG cc_start: 0.8311 (tpt90) cc_final: 0.7959 (tpt90) REVERT: C 14 LYS cc_start: 0.7807 (tptt) cc_final: 0.7562 (tppt) REVERT: C 42 GLU cc_start: 0.8143 (tp30) cc_final: 0.7885 (tp30) REVERT: D 48 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7809 (mp10) REVERT: D 63 MET cc_start: 0.8820 (mmm) cc_final: 0.8524 (mmm) REVERT: D 69 ASP cc_start: 0.8129 (t0) cc_final: 0.7851 (t0) REVERT: D 121 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8387 (tttm) REVERT: E 82 ASP cc_start: 0.8449 (t70) cc_final: 0.8148 (t0) REVERT: F 54 GLU cc_start: 0.7661 (tp30) cc_final: 0.7416 (tp30) REVERT: F 86 ASP cc_start: 0.8513 (m-30) cc_final: 0.8309 (m-30) REVERT: G 73 ASP cc_start: 0.8404 (m-30) cc_final: 0.7964 (m-30) REVERT: H 68 ASN cc_start: 0.9098 (m-40) cc_final: 0.8686 (m110) outliers start: 15 outliers final: 9 residues processed: 217 average time/residue: 0.1507 time to fit residues: 44.9856 Evaluate side-chains 211 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 3.9990 chunk 133 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 overall best weight: 0.7372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.069904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060316 restraints weight = 75523.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061766 restraints weight = 35779.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062691 restraints weight = 22014.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063279 restraints weight = 15888.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063614 restraints weight = 12837.725| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16820 Z= 0.157 Angle : 0.587 6.233 24147 Z= 0.341 Chirality : 0.040 0.180 2837 Planarity : 0.005 0.049 2185 Dihedral : 27.143 73.999 4753 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.16 % Allowed : 13.28 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1537 helix: 2.13 (0.21), residues: 634 sheet: -0.82 (0.30), residues: 306 loop : -0.43 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.038 0.002 TYR D 84 PHE 0.009 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (16820) covalent geometry : angle 0.58678 / 0.34 (24147) hydrogen bonds : bond 0.04626 / 3.03 ( 936) hydrogen bonds : angle 3.76721 / 2.68 ( 2360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8314 (mmp) cc_final: 0.7993 (mmp) REVERT: A 130 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7869 (tpt90) REVERT: C 33 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8214 (mtp180) REVERT: D 48 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7773 (mp10) REVERT: D 63 MET cc_start: 0.8755 (mmm) cc_final: 0.8500 (mmm) REVERT: D 69 ASP cc_start: 0.8130 (t0) cc_final: 0.7849 (t0) REVERT: D 121 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8476 (tttm) REVERT: E 82 ASP cc_start: 0.8384 (t70) cc_final: 0.8113 (t0) REVERT: F 86 ASP cc_start: 0.8521 (m-30) cc_final: 0.8319 (m-30) REVERT: G 73 ASP cc_start: 0.8298 (m-30) cc_final: 0.7873 (m-30) REVERT: H 68 ASN cc_start: 0.9031 (m-40) cc_final: 0.8684 (m-40) REVERT: H 106 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7031 (mm-30) REVERT: H 109 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8136 (ptpp) outliers start: 15 outliers final: 12 residues processed: 214 average time/residue: 0.1420 time to fit residues: 42.1002 Evaluate side-chains 216 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 103 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 26 ASN B 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.070077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060604 restraints weight = 75374.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062052 restraints weight = 35775.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062970 restraints weight = 21919.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063556 restraints weight = 15854.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.063938 restraints weight = 12784.976| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16820 Z= 0.143 Angle : 0.566 12.672 24147 Z= 0.332 Chirality : 0.040 0.178 2837 Planarity : 0.005 0.045 2185 Dihedral : 27.044 72.892 4753 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.89 % Allowed : 13.42 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1537 helix: 2.29 (0.21), residues: 634 sheet: -0.63 (0.30), residues: 308 loop : -0.30 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 36 TYR 0.055 0.002 TYR D 84 PHE 0.009 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (16820) covalent geometry : angle 0.56586 / 0.33 (24147) hydrogen bonds : bond 0.04108 / 2.67 ( 936) hydrogen bonds : angle 3.56257 / 2.54 ( 2360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8327 (mmp) cc_final: 0.7933 (mmt) REVERT: A 130 ARG cc_start: 0.8130 (tpt90) cc_final: 0.7904 (tpt90) REVERT: D 48 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7776 (mp10) REVERT: D 63 MET cc_start: 0.8763 (mmm) cc_final: 0.8509 (mmm) REVERT: D 69 ASP cc_start: 0.8110 (t0) cc_final: 0.7836 (t0) REVERT: D 121 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8495 (tttm) REVERT: E 51 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7701 (mm-30) REVERT: E 82 ASP cc_start: 0.8386 (t70) cc_final: 0.8110 (t0) REVERT: F 86 ASP cc_start: 0.8486 (m-30) cc_final: 0.8282 (m-30) REVERT: G 69 ASN cc_start: 0.8894 (m-40) cc_final: 0.8097 (m110) REVERT: G 73 ASP cc_start: 0.8334 (m-30) cc_final: 0.7954 (m-30) REVERT: H 68 ASN cc_start: 0.9017 (m-40) cc_final: 0.8632 (m110) REVERT: H 81 LEU cc_start: 0.9153 (mt) cc_final: 0.8892 (mt) REVERT: H 109 LYS cc_start: 0.8417 (ptpp) cc_final: 0.8137 (ptpp) outliers start: 20 outliers final: 14 residues processed: 214 average time/residue: 0.1397 time to fit residues: 41.3930 Evaluate side-chains 218 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.068761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.059302 restraints weight = 75725.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060752 restraints weight = 36274.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061669 restraints weight = 22200.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062248 restraints weight = 16094.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062586 restraints weight = 12995.367| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16820 Z= 0.194 Angle : 0.608 10.070 24147 Z= 0.350 Chirality : 0.041 0.198 2837 Planarity : 0.005 0.044 2185 Dihedral : 27.119 74.953 4753 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.31 % Allowed : 13.85 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.22), residues: 1537 helix: 2.29 (0.21), residues: 634 sheet: -0.72 (0.30), residues: 318 loop : -0.33 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 36 TYR 0.051 0.002 TYR D 84 PHE 0.008 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (16820) covalent geometry : angle 0.60835 / 0.35 (24147) hydrogen bonds : bond 0.04864 / 3.19 ( 936) hydrogen bonds : angle 3.67165 / 2.63 ( 2360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8340 (mmp) cc_final: 0.7935 (mmt) REVERT: A 130 ARG cc_start: 0.8168 (tpt90) cc_final: 0.7915 (tpt90) REVERT: C 41 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8263 (m) REVERT: D 48 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7815 (mp10) REVERT: D 63 MET cc_start: 0.8785 (mmm) cc_final: 0.8572 (mmm) REVERT: D 69 ASP cc_start: 0.8084 (t0) cc_final: 0.7799 (t0) REVERT: D 121 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8500 (tttm) REVERT: E 51 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 82 ASP cc_start: 0.8437 (t70) cc_final: 0.8160 (t0) REVERT: G 41 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8876 (t) REVERT: H 68 ASN cc_start: 0.9027 (m-40) cc_final: 0.8648 (m110) REVERT: H 109 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8205 (ptpp) outliers start: 16 outliers final: 12 residues processed: 210 average time/residue: 0.1405 time to fit residues: 40.6396 Evaluate side-chains 215 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 8.9990 chunk 167 optimal weight: 0.0070 chunk 170 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN C 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059706 restraints weight = 75587.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061149 restraints weight = 35967.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.062073 restraints weight = 21977.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062652 restraints weight = 15827.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.062982 restraints weight = 12792.166| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16820 Z= 0.155 Angle : 0.573 8.073 24147 Z= 0.337 Chirality : 0.040 0.187 2837 Planarity : 0.004 0.047 2185 Dihedral : 27.054 73.450 4753 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.16 % Allowed : 14.86 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1537 helix: 2.33 (0.21), residues: 634 sheet: -0.64 (0.30), residues: 308 loop : -0.27 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.064 0.002 TYR D 84 PHE 0.008 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (16820) covalent geometry : angle 0.57254 / 0.34 (24147) hydrogen bonds : bond 0.04188 / 2.73 ( 936) hydrogen bonds : angle 3.56541 / 2.54 ( 2360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8334 (mmp) cc_final: 0.7937 (mmt) REVERT: A 130 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7908 (tpt90) REVERT: C 41 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8241 (m) REVERT: D 48 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7812 (mp10) REVERT: D 63 MET cc_start: 0.8770 (mmm) cc_final: 0.8504 (mmm) REVERT: D 69 ASP cc_start: 0.8075 (t0) cc_final: 0.7809 (t0) REVERT: D 121 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8517 (tttm) REVERT: E 51 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7696 (mm-30) REVERT: E 82 ASP cc_start: 0.8427 (t70) cc_final: 0.8145 (t0) REVERT: G 41 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8843 (t) REVERT: H 68 ASN cc_start: 0.9007 (m-40) cc_final: 0.8629 (m110) REVERT: H 81 LEU cc_start: 0.9123 (mt) cc_final: 0.8872 (mt) REVERT: H 109 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8199 (ptpp) outliers start: 15 outliers final: 11 residues processed: 213 average time/residue: 0.1390 time to fit residues: 40.8451 Evaluate side-chains 215 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 0.0050 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 26 ASN B 28 GLN G 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.069139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059810 restraints weight = 75309.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061244 restraints weight = 35664.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062167 restraints weight = 21859.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062743 restraints weight = 15768.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063067 restraints weight = 12735.653| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16820 Z= 0.148 Angle : 0.572 8.580 24147 Z= 0.337 Chirality : 0.040 0.188 2837 Planarity : 0.005 0.045 2185 Dihedral : 27.010 72.697 4753 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.02 % Allowed : 15.44 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1537 helix: 2.29 (0.21), residues: 634 sheet: -0.55 (0.30), residues: 304 loop : -0.18 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.081 0.002 TYR D 84 PHE 0.007 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (16820) covalent geometry : angle 0.57220 / 0.34 (24147) hydrogen bonds : bond 0.04183 / 2.72 ( 936) hydrogen bonds : angle 3.54319 / 2.53 ( 2360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8327 (mmp) cc_final: 0.7925 (mmt) REVERT: A 130 ARG cc_start: 0.8139 (tpt90) cc_final: 0.7883 (tpt90) REVERT: C 41 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8200 (m) REVERT: D 48 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7805 (mp10) REVERT: D 63 MET cc_start: 0.8760 (mmm) cc_final: 0.8491 (mmm) REVERT: D 69 ASP cc_start: 0.8083 (t0) cc_final: 0.7802 (t0) REVERT: D 121 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8512 (tttm) REVERT: E 51 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7712 (mm-30) REVERT: E 82 ASP cc_start: 0.8431 (t70) cc_final: 0.8152 (t0) REVERT: G 41 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8958 (t) REVERT: H 68 ASN cc_start: 0.9003 (m-40) cc_final: 0.8627 (m110) REVERT: H 81 LEU cc_start: 0.9107 (mt) cc_final: 0.8838 (mt) REVERT: H 109 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8205 (ptpp) outliers start: 14 outliers final: 11 residues processed: 210 average time/residue: 0.1377 time to fit residues: 40.1943 Evaluate side-chains 213 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN C 105 GLN G 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.068951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059671 restraints weight = 75245.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061109 restraints weight = 35741.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062014 restraints weight = 21870.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062588 restraints weight = 15795.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062871 restraints weight = 12781.206| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16820 Z= 0.155 Angle : 0.574 8.570 24147 Z= 0.338 Chirality : 0.040 0.190 2837 Planarity : 0.004 0.048 2185 Dihedral : 26.995 72.675 4753 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 15.44 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1537 helix: 2.30 (0.21), residues: 634 sheet: -0.54 (0.30), residues: 304 loop : -0.17 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.074 0.002 TYR D 84 PHE 0.007 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (16820) covalent geometry : angle 0.57427 / 0.34 (24147) hydrogen bonds : bond 0.04226 / 2.75 ( 936) hydrogen bonds : angle 3.53974 / 2.53 ( 2360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.16 seconds wall clock time: 46 minutes 45.05 seconds (2805.05 seconds total)