Starting phenix.real_space_refine on Fri Jul 3 18:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2m_53532/07_2026/9r2m_53532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2m_53532/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2m_53532/07_2026/9r2m_53532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2m_53532/07_2026/9r2m_53532.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2m_53532/07_2026/9r2m_53532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2m_53532/07_2026/9r2m_53532.cif" } 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-dev-6108/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: 3.22, per 1000 atoms: 0.20 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: 1.25 Conformation dependent library (CDL) restraints added in 493.9 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: 2.14 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: 1.65 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: 21289 0.91 - 1.81: 2128 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: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- 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 : 0.667 4.534 24147 Z= 0.556 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 0.66704 / 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 : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8231 (tpt90) cc_final: 0.7837 (tpt90) REVERT: B 51 ILE cc_start: 0.8981 (mm) cc_final: 0.8678 (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: 0.8003 (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: 0.7693 (mm-30) REVERT: D 58 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8638 (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 43 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7411 (mtp85) REVERT: E 61 LEU cc_start: 0.8738 (mt) cc_final: 0.8468 (mt) REVERT: E 78 ASP cc_start: 0.8246 (m-30) cc_final: 0.7906 (t0) REVERT: E 94 GLN cc_start: 0.8599 (mt0) cc_final: 0.7920 (mt0) REVERT: F 54 GLU cc_start: 0.8204 (tp30) cc_final: 0.7970 (tp30) REVERT: F 86 ASP cc_start: 0.8522 (m-30) cc_final: 0.8304 (m-30) REVERT: G 51 TYR cc_start: 0.9040 (t80) cc_final: 0.8785 (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: 0.8455 (t70) REVERT: G 96 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8139 (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: 0.1660 time to fit residues: 60.4491 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 : 0.491 ------------------------------------------------------------------------------- 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: 9.9990 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 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 = 0.3660 r_free = 0.3660 target = 0.074427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063740 restraints weight = 76871.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065290 restraints weight = 36271.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066291 restraints weight = 21861.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066918 restraints weight = 15531.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067277 restraints weight = 12466.339| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16820 Z= 0.309 Angle : 0.854 9.450 24147 Z= 0.468 Chirality : 0.053 0.252 2837 Planarity : 0.007 0.049 2185 Dihedral : 26.993 77.190 4757 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.74 % Allowed : 6.78 % Favored : 90.48 % 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: -0.62 (0.20), residues: 1537 helix: 0.76 (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 0.008 0.001 ARG E 130 TYR 0.021 0.002 TYR B 89 PHE 0.021 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 0.00610 / 0.31 (16820) covalent geometry : angle 0.85448 / 0.47 (24147) hydrogen bonds : bond 0.07967 / 5.15 ( 936) hydrogen bonds : angle 4.70528 / 3.35 ( 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 232 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8355 (tpt90) cc_final: 0.8002 (tpt90) REVERT: C 42 GLU cc_start: 0.8068 (tp30) cc_final: 0.7772 (tp30) REVERT: C 69 ASN cc_start: 0.8302 (m-40) cc_final: 0.8034 (m-40) REVERT: C 73 ASP cc_start: 0.8883 (m-30) cc_final: 0.8467 (m-30) REVERT: D 34 ARG cc_start: 0.6734 (mtt-85) cc_final: 0.6340 (ttm110) REVERT: D 36 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7330 (mm-30) REVERT: D 48 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7597 (mp10) REVERT: D 69 ASP cc_start: 0.8140 (t0) cc_final: 0.7761 (t0) REVERT: D 90 ILE cc_start: 0.8787 (mm) cc_final: 0.8578 (mt) REVERT: E 63 ILE cc_start: 0.9033 (mt) cc_final: 0.8662 (mt) REVERT: E 69 GLN cc_start: 0.8710 (mt0) cc_final: 0.8467 (tt0) REVERT: E 78 ASP cc_start: 0.8455 (m-30) cc_final: 0.8184 (t0) REVERT: E 124 ASP cc_start: 0.8761 (m-30) cc_final: 0.8530 (m-30) REVERT: F 31 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8283 (p) REVERT: F 32 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8795 (tttm) REVERT: F 54 GLU cc_start: 0.7715 (tp30) cc_final: 0.7441 (tp30) REVERT: F 86 ASP cc_start: 0.8583 (m-30) cc_final: 0.8336 (m-30) REVERT: G 51 TYR cc_start: 0.9202 (t80) cc_final: 0.8829 (t80) REVERT: G 63 ILE cc_start: 0.9287 (mt) cc_final: 0.9081 (mm) REVERT: G 74 ASN cc_start: 0.8844 (m-40) cc_final: 0.8609 (m-40) REVERT: H 68 ASN cc_start: 0.9127 (m-40) cc_final: 0.8780 (m110) REVERT: H 100 ARG cc_start: 0.8739 (mtt-85) cc_final: 0.8528 (mtt-85) outliers start: 19 outliers final: 12 residues processed: 222 average time/residue: 0.1400 time to fit residues: 43.3374 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 : 0.341 ------------------------------------------------------------------------------- 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: 0.0370 chunk 23 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 0.0570 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 28 GLN C 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.075822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065081 restraints weight = 76426.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066653 restraints weight = 35740.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067660 restraints weight = 21581.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.068316 restraints weight = 15435.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068688 restraints weight = 12306.573| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16820 Z= 0.148 Angle : 0.555 5.810 24147 Z= 0.335 Chirality : 0.040 0.160 2837 Planarity : 0.004 0.037 2185 Dihedral : 26.903 74.743 4753 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.73 % Allowed : 9.96 % Favored : 88.31 % 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: 0.38 (0.21), residues: 1537 helix: 1.77 (0.21), residues: 620 sheet: -0.79 (0.29), residues: 312 loop : -0.70 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.024 0.001 TYR B 89 PHE 0.007 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.15 (16820) covalent geometry : angle 0.55527 / 0.34 (24147) hydrogen bonds : bond 0.05068 / 3.35 ( 936) hydrogen bonds : angle 3.99134 / 2.84 ( 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 225 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8315 (mmp) cc_final: 0.7939 (mmt) REVERT: A 130 ARG cc_start: 0.8303 (tpt90) cc_final: 0.7948 (tpt90) REVERT: B 85 MET cc_start: 0.8160 (mmp) cc_final: 0.7862 (mmp) REVERT: B 89 TYR cc_start: 0.8120 (m-10) cc_final: 0.7844 (m-10) REVERT: C 42 GLU cc_start: 0.8078 (tp30) cc_final: 0.7765 (tp30) REVERT: D 48 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7587 (mp10) REVERT: D 63 MET cc_start: 0.8762 (mmm) cc_final: 0.8501 (mmm) REVERT: D 69 ASP cc_start: 0.8097 (t0) cc_final: 0.7756 (t0) REVERT: D 90 ILE cc_start: 0.8566 (mm) cc_final: 0.8366 (mt) REVERT: D 121 LYS cc_start: 0.8900 (tttt) cc_final: 0.8616 (tttm) REVERT: E 78 ASP cc_start: 0.8449 (m-30) cc_final: 0.8210 (t0) REVERT: E 82 ASP cc_start: 0.8051 (t0) cc_final: 0.7721 (t0) REVERT: F 31 THR cc_start: 0.8512 (p) cc_final: 0.8246 (p) REVERT: F 54 GLU cc_start: 0.7572 (tp30) cc_final: 0.7369 (tp30) REVERT: F 86 ASP cc_start: 0.8515 (m-30) cc_final: 0.8306 (m-30) REVERT: G 74 ASN cc_start: 0.8827 (m-40) cc_final: 0.8505 (m-40) REVERT: G 91 ASP cc_start: 0.8398 (t0) cc_final: 0.8017 (t0) REVERT: H 68 ASN cc_start: 0.9101 (m-40) cc_final: 0.8779 (m-40) REVERT: H 69 ASP cc_start: 0.8474 (t0) cc_final: 0.8236 (t0) REVERT: H 106 GLU cc_start: 0.7813 (tp30) cc_final: 0.6880 (mm-30) outliers start: 12 outliers final: 6 residues processed: 218 average time/residue: 0.1388 time to fit residues: 42.2873 Evaluate side-chains 206 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 200 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR 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 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.071463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061233 restraints weight = 76447.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062758 restraints weight = 35858.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063747 restraints weight = 21900.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064353 restraints weight = 15629.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064650 restraints weight = 12638.223| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16820 Z= 0.227 Angle : 0.685 9.828 24147 Z= 0.390 Chirality : 0.044 0.208 2837 Planarity : 0.005 0.055 2185 Dihedral : 27.341 84.578 4753 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.31 % Allowed : 10.53 % Favored : 87.16 % 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: 0.36 (0.21), residues: 1537 helix: 1.81 (0.21), residues: 630 sheet: -1.11 (0.29), residues: 306 loop : -0.64 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 93 TYR 0.023 0.002 TYR D 122 PHE 0.014 0.001 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.002 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (16820) covalent geometry : angle 0.68489 / 0.39 (24147) hydrogen bonds : bond 0.06544 / 4.29 ( 936) hydrogen bonds : angle 4.11307 / 2.94 ( 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 222 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8327 (tpt90) cc_final: 0.7971 (tpt90) REVERT: B 85 MET cc_start: 0.8423 (mmp) cc_final: 0.8140 (mmt) REVERT: C 42 GLU cc_start: 0.8108 (tp30) cc_final: 0.7858 (tp30) REVERT: D 48 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7853 (mp10) REVERT: D 58 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8307 (mtmm) REVERT: D 63 MET cc_start: 0.8830 (mmm) cc_final: 0.8588 (mmm) REVERT: D 69 ASP cc_start: 0.8114 (t0) cc_final: 0.7807 (t0) REVERT: D 121 LYS cc_start: 0.8946 (tttt) cc_final: 0.8637 (tttm) REVERT: E 82 ASP cc_start: 0.8330 (t0) cc_final: 0.7964 (t0) REVERT: F 54 GLU cc_start: 0.7843 (tp30) cc_final: 0.7570 (tp30) REVERT: F 86 ASP cc_start: 0.8519 (m-30) cc_final: 0.8267 (m-30) REVERT: G 73 ASP cc_start: 0.8405 (m-30) cc_final: 0.8027 (m-30) REVERT: G 74 ASN cc_start: 0.8834 (m-40) cc_final: 0.8629 (m-40) REVERT: H 68 ASN cc_start: 0.9089 (m-40) cc_final: 0.8720 (m110) REVERT: H 69 ASP cc_start: 0.8588 (t0) cc_final: 0.8332 (t0) REVERT: H 77 GLU cc_start: 0.8075 (tp30) cc_final: 0.7724 (tp30) outliers start: 16 outliers final: 11 residues processed: 213 average time/residue: 0.1342 time to fit residues: 39.7954 Evaluate side-chains 211 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.072021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061904 restraints weight = 76026.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063442 restraints weight = 35492.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064425 restraints weight = 21476.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065049 restraints weight = 15368.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065420 restraints weight = 12375.808| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16820 Z= 0.154 Angle : 0.549 5.376 24147 Z= 0.330 Chirality : 0.040 0.169 2837 Planarity : 0.005 0.059 2185 Dihedral : 27.181 74.792 4753 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.02 % Allowed : 11.98 % Favored : 86.00 % 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: 0.81 (0.21), residues: 1537 helix: 2.15 (0.21), residues: 634 sheet: -0.81 (0.29), residues: 310 loop : -0.41 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.023 0.002 TYR B 89 PHE 0.018 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (16820) covalent geometry : angle 0.54941 / 0.33 (24147) hydrogen bonds : bond 0.04402 / 2.90 ( 936) hydrogen bonds : angle 3.72860 / 2.64 ( 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 224 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8293 (mmp) cc_final: 0.8030 (mmp) REVERT: A 130 ARG cc_start: 0.8281 (tpt90) cc_final: 0.7926 (tpt90) REVERT: C 42 GLU cc_start: 0.8103 (tp30) cc_final: 0.7825 (tp30) REVERT: D 48 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7757 (mp10) REVERT: D 58 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8178 (mtmm) REVERT: D 63 MET cc_start: 0.8814 (mmm) cc_final: 0.8521 (mmm) REVERT: D 69 ASP cc_start: 0.8134 (t0) cc_final: 0.7810 (t0) REVERT: D 121 LYS cc_start: 0.8896 (tttt) cc_final: 0.8457 (tttm) REVERT: E 82 ASP cc_start: 0.8344 (t0) cc_final: 0.7968 (t0) REVERT: F 86 ASP cc_start: 0.8537 (m-30) cc_final: 0.8307 (m-30) REVERT: G 73 ASP cc_start: 0.8335 (m-30) cc_final: 0.7916 (m-30) REVERT: G 74 ASN cc_start: 0.8831 (m-40) cc_final: 0.8611 (m-40) REVERT: G 91 ASP cc_start: 0.8507 (t70) cc_final: 0.8279 (t0) REVERT: H 68 ASN cc_start: 0.9089 (m-40) cc_final: 0.8722 (m-40) REVERT: H 69 ASP cc_start: 0.8583 (t0) cc_final: 0.8284 (t0) REVERT: H 77 GLU cc_start: 0.8082 (tp30) cc_final: 0.7622 (tp30) REVERT: H 106 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7116 (mm-30) REVERT: H 109 LYS cc_start: 0.8785 (ptmm) cc_final: 0.8535 (ptpp) outliers start: 14 outliers final: 9 residues processed: 216 average time/residue: 0.1435 time to fit residues: 42.8043 Evaluate side-chains 213 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.071275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061329 restraints weight = 75353.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062845 restraints weight = 35113.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063825 restraints weight = 21255.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064451 restraints weight = 15215.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064843 restraints weight = 12186.137| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16820 Z= 0.160 Angle : 0.571 7.838 24147 Z= 0.337 Chirality : 0.040 0.175 2837 Planarity : 0.005 0.052 2185 Dihedral : 27.121 75.267 4753 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.60 % Allowed : 11.69 % Favored : 85.71 % 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: 1.00 (0.22), residues: 1537 helix: 2.27 (0.20), residues: 636 sheet: -0.64 (0.29), residues: 316 loop : -0.32 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 80 TYR 0.029 0.002 TYR B 89 PHE 0.009 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (16820) covalent geometry : angle 0.57144 / 0.34 (24147) hydrogen bonds : bond 0.04743 / 3.10 ( 936) hydrogen bonds : angle 3.61441 / 2.57 ( 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 223 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8273 (mmp) cc_final: 0.7986 (mmp) REVERT: A 130 ARG cc_start: 0.8315 (tpt90) cc_final: 0.7953 (tpt90) REVERT: C 42 GLU cc_start: 0.8121 (tp30) cc_final: 0.7839 (tp30) REVERT: D 48 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7705 (mp10) REVERT: D 58 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8186 (mtmm) REVERT: D 63 MET cc_start: 0.8810 (mmm) cc_final: 0.8530 (mmm) REVERT: D 69 ASP cc_start: 0.8134 (t0) cc_final: 0.7802 (t0) REVERT: D 121 LYS cc_start: 0.8876 (tttt) cc_final: 0.8563 (tttm) REVERT: E 51 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7807 (mm-30) REVERT: E 82 ASP cc_start: 0.8394 (t0) cc_final: 0.8002 (t0) REVERT: F 86 ASP cc_start: 0.8578 (m-30) cc_final: 0.8315 (m-30) REVERT: G 73 ASP cc_start: 0.8417 (m-30) cc_final: 0.8054 (m-30) REVERT: G 74 ASN cc_start: 0.8806 (m-40) cc_final: 0.8580 (m-40) REVERT: G 91 ASP cc_start: 0.8357 (t70) cc_final: 0.8105 (t0) REVERT: H 68 ASN cc_start: 0.9110 (m-40) cc_final: 0.8753 (m-40) REVERT: H 69 ASP cc_start: 0.8616 (t0) cc_final: 0.8283 (t0) REVERT: H 77 GLU cc_start: 0.8110 (tp30) cc_final: 0.7662 (tp30) REVERT: H 106 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7019 (mm-30) REVERT: H 109 LYS cc_start: 0.8788 (ptmm) cc_final: 0.8531 (ptpp) outliers start: 18 outliers final: 14 residues processed: 210 average time/residue: 0.1405 time to fit residues: 41.0508 Evaluate side-chains 213 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR 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 74 GLU Chi-restraints excluded: chain E residue 87 SER 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 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: 8.9990 chunk 15 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 26 ASN B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.071310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.061483 restraints weight = 75311.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063005 restraints weight = 35360.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063979 restraints weight = 21305.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064586 restraints weight = 15220.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064992 restraints weight = 12238.180| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16820 Z= 0.145 Angle : 0.528 6.127 24147 Z= 0.320 Chirality : 0.039 0.161 2837 Planarity : 0.004 0.050 2185 Dihedral : 27.040 72.444 4753 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.31 % Allowed : 12.55 % Favored : 85.14 % 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: 1.22 (0.22), residues: 1537 helix: 2.45 (0.20), residues: 634 sheet: -0.53 (0.29), residues: 318 loop : -0.16 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.020 0.001 TYR B 89 PHE 0.009 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (16820) covalent geometry : angle 0.52837 / 0.32 (24147) hydrogen bonds : bond 0.03990 / 2.60 ( 936) hydrogen bonds : angle 3.43180 / 2.43 ( 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 220 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8321 (mmp) cc_final: 0.7953 (mmt) REVERT: A 130 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7992 (tpt90) REVERT: C 14 LYS cc_start: 0.7885 (tptt) cc_final: 0.7629 (tppt) REVERT: C 42 GLU cc_start: 0.8106 (tp30) cc_final: 0.7798 (tp30) REVERT: C 51 TYR cc_start: 0.8475 (t80) cc_final: 0.8060 (t80) REVERT: D 48 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7779 (mp10) REVERT: D 58 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8162 (mtmm) REVERT: D 63 MET cc_start: 0.8793 (mmm) cc_final: 0.8514 (mmm) REVERT: D 69 ASP cc_start: 0.8123 (t0) cc_final: 0.7818 (t0) REVERT: D 121 LYS cc_start: 0.8859 (tttt) cc_final: 0.8539 (tttm) REVERT: E 51 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7761 (mm-30) REVERT: E 82 ASP cc_start: 0.8406 (t0) cc_final: 0.8036 (t0) REVERT: F 86 ASP cc_start: 0.8571 (m-30) cc_final: 0.8326 (m-30) REVERT: G 73 ASP cc_start: 0.8416 (m-30) cc_final: 0.7981 (m-30) REVERT: G 74 ASN cc_start: 0.8807 (m-40) cc_final: 0.8580 (m-40) REVERT: H 68 ASN cc_start: 0.9096 (m-40) cc_final: 0.8737 (m-40) REVERT: H 69 ASP cc_start: 0.8566 (t0) cc_final: 0.8227 (t0) REVERT: H 77 GLU cc_start: 0.8070 (tp30) cc_final: 0.7628 (tp30) REVERT: H 106 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7057 (mm-30) REVERT: H 109 LYS cc_start: 0.8773 (ptmm) cc_final: 0.8562 (ptpp) outliers start: 16 outliers final: 12 residues processed: 210 average time/residue: 0.1352 time to fit residues: 39.6741 Evaluate side-chains 210 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU 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: 6.9990 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 161 optimal weight: 0.0070 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.5406 ------------------------------------------------------------------------------- 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 ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.071143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061387 restraints weight = 75481.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062915 restraints weight = 35128.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.063868 restraints weight = 21115.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064476 restraints weight = 15120.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064862 restraints weight = 12147.250| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16820 Z= 0.138 Angle : 0.533 7.038 24147 Z= 0.321 Chirality : 0.039 0.160 2837 Planarity : 0.004 0.045 2185 Dihedral : 26.948 71.762 4753 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 13.28 % Favored : 84.70 % 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: 1.36 (0.22), residues: 1537 helix: 2.52 (0.20), residues: 636 sheet: -0.41 (0.30), residues: 318 loop : -0.09 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 80 TYR 0.031 0.002 TYR B 89 PHE 0.007 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (16820) covalent geometry : angle 0.53299 / 0.32 (24147) hydrogen bonds : bond 0.03943 / 2.57 ( 936) hydrogen bonds : angle 3.35830 / 2.38 ( 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 218 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8301 (mmp) cc_final: 0.7935 (mmt) REVERT: A 130 ARG cc_start: 0.8276 (tpt90) cc_final: 0.7993 (tpt90) REVERT: C 14 LYS cc_start: 0.7906 (tptt) cc_final: 0.7695 (tppt) REVERT: C 16 LYS cc_start: 0.9244 (ttpt) cc_final: 0.8978 (ttmm) REVERT: C 42 GLU cc_start: 0.8116 (tp30) cc_final: 0.7806 (tp30) REVERT: D 48 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7814 (mp10) REVERT: D 58 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8158 (mtmm) REVERT: D 63 MET cc_start: 0.8795 (mmm) cc_final: 0.8512 (mmm) REVERT: D 69 ASP cc_start: 0.8125 (t0) cc_final: 0.7815 (t0) REVERT: D 121 LYS cc_start: 0.8880 (tttt) cc_final: 0.8582 (tttm) REVERT: E 51 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7745 (mm-30) REVERT: E 82 ASP cc_start: 0.8438 (t0) cc_final: 0.8044 (t0) REVERT: F 86 ASP cc_start: 0.8572 (m-30) cc_final: 0.8315 (m-30) REVERT: G 73 ASP cc_start: 0.8406 (m-30) cc_final: 0.7973 (m-30) REVERT: G 74 ASN cc_start: 0.8765 (m-40) cc_final: 0.8549 (m-40) REVERT: H 68 ASN cc_start: 0.9103 (m-40) cc_final: 0.8737 (m-40) REVERT: H 69 ASP cc_start: 0.8556 (t0) cc_final: 0.8213 (t0) REVERT: H 77 GLU cc_start: 0.8091 (tp30) cc_final: 0.7667 (tp30) REVERT: H 106 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6893 (mm-30) REVERT: H 109 LYS cc_start: 0.8774 (ptmm) cc_final: 0.8525 (ptpp) outliers start: 14 outliers final: 12 residues processed: 209 average time/residue: 0.1451 time to fit residues: 42.2518 Evaluate side-chains 214 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 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 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: 6.9990 chunk 167 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 38 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 26 ASN B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.068712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059241 restraints weight = 75927.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060700 restraints weight = 35645.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061624 restraints weight = 21778.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062215 restraints weight = 15695.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062587 restraints weight = 12643.759| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16820 Z= 0.202 Angle : 0.606 8.776 24147 Z= 0.353 Chirality : 0.041 0.195 2837 Planarity : 0.005 0.044 2185 Dihedral : 27.178 76.757 4753 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.16 % Allowed : 13.71 % Favored : 84.13 % 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: 2.32 (0.20), residues: 636 sheet: -0.62 (0.30), residues: 308 loop : -0.16 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.035 0.002 TYR D 84 PHE 0.012 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.017 0.002 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 (16820) covalent geometry : angle 0.60606 / 0.35 (24147) hydrogen bonds : bond 0.05187 / 3.42 ( 936) hydrogen bonds : angle 3.67487 / 2.62 ( 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 216 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8344 (mmp) cc_final: 0.7941 (mmt) REVERT: A 130 ARG cc_start: 0.8267 (tpt90) cc_final: 0.7984 (tpt90) REVERT: C 16 LYS cc_start: 0.9305 (ttpt) cc_final: 0.9050 (ttmm) REVERT: D 48 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7801 (mp10) REVERT: D 58 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8210 (mtmm) REVERT: D 63 MET cc_start: 0.8828 (mmm) cc_final: 0.8596 (mmm) REVERT: D 69 ASP cc_start: 0.8161 (t0) cc_final: 0.7836 (t0) REVERT: D 121 LYS cc_start: 0.8889 (tttt) cc_final: 0.8580 (tttm) REVERT: E 51 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7701 (mm-30) REVERT: E 82 ASP cc_start: 0.8438 (t0) cc_final: 0.8233 (t0) REVERT: G 73 ASP cc_start: 0.8413 (m-30) cc_final: 0.8002 (m-30) REVERT: G 74 ASN cc_start: 0.8850 (m-40) cc_final: 0.8631 (m-40) REVERT: H 68 ASN cc_start: 0.9081 (m-40) cc_final: 0.8681 (m110) REVERT: H 69 ASP cc_start: 0.8595 (t0) cc_final: 0.8308 (t0) REVERT: H 77 GLU cc_start: 0.8125 (tp30) cc_final: 0.7666 (tp30) REVERT: H 106 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7389 (mm-30) REVERT: H 109 LYS cc_start: 0.8762 (ptmm) cc_final: 0.8523 (ptpp) outliers start: 15 outliers final: 13 residues processed: 206 average time/residue: 0.1481 time to fit residues: 42.4450 Evaluate side-chains 210 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 THR 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 F residue 97 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 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: 0.8980 chunk 160 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.0030 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.069617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060061 restraints weight = 75590.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061565 restraints weight = 35262.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062510 restraints weight = 21306.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063117 restraints weight = 15273.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063486 restraints weight = 12206.125| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16820 Z= 0.142 Angle : 0.557 8.447 24147 Z= 0.332 Chirality : 0.040 0.180 2837 Planarity : 0.004 0.043 2185 Dihedral : 27.076 73.743 4753 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.73 % Allowed : 14.00 % Favored : 84.27 % 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: 1.26 (0.22), residues: 1537 helix: 2.44 (0.20), residues: 636 sheet: -0.54 (0.30), residues: 318 loop : -0.09 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.059 0.002 TYR H 84 PHE 0.008 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (16820) covalent geometry : angle 0.55739 / 0.33 (24147) hydrogen bonds : bond 0.04104 / 2.69 ( 936) hydrogen bonds : angle 3.48559 / 2.47 ( 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 220 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8280 (tpt90) cc_final: 0.7989 (tpt90) REVERT: C 16 LYS cc_start: 0.9298 (ttpt) cc_final: 0.9039 (ttmm) REVERT: D 48 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7789 (mp10) REVERT: D 58 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8173 (mtmm) REVERT: D 63 MET cc_start: 0.8828 (mmm) cc_final: 0.8545 (mmm) REVERT: D 69 ASP cc_start: 0.8141 (t0) cc_final: 0.7843 (t0) REVERT: D 121 LYS cc_start: 0.8881 (tttt) cc_final: 0.8583 (tttm) REVERT: E 51 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7640 (mm-30) REVERT: G 69 ASN cc_start: 0.8945 (m-40) cc_final: 0.8157 (m110) REVERT: G 73 ASP cc_start: 0.8413 (m-30) cc_final: 0.7983 (m-30) REVERT: G 74 ASN cc_start: 0.8794 (m-40) cc_final: 0.8584 (m-40) REVERT: H 68 ASN cc_start: 0.9079 (m-40) cc_final: 0.8672 (m110) REVERT: H 69 ASP cc_start: 0.8588 (t0) cc_final: 0.8345 (t0) REVERT: H 77 GLU cc_start: 0.8135 (tp30) cc_final: 0.7674 (tp30) REVERT: H 106 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7319 (mm-30) REVERT: H 109 LYS cc_start: 0.8739 (ptmm) cc_final: 0.8490 (ptpp) outliers start: 12 outliers final: 11 residues processed: 215 average time/residue: 0.1424 time to fit residues: 43.0766 Evaluate side-chains 213 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 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 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: 0.1980 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.069441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060098 restraints weight = 75150.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061543 restraints weight = 35659.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062451 restraints weight = 21818.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063018 restraints weight = 15813.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063378 restraints weight = 12805.764| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5341 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= 0.151 Angle : 0.558 8.506 24147 Z= 0.333 Chirality : 0.039 0.179 2837 Planarity : 0.005 0.043 2185 Dihedral : 27.023 72.772 4753 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.88 % Allowed : 14.72 % Favored : 83.41 % 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: 1.25 (0.22), residues: 1537 helix: 2.41 (0.20), residues: 636 sheet: -0.59 (0.30), residues: 322 loop : -0.03 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.078 0.002 TYR F 89 PHE 0.006 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (16820) covalent geometry : angle 0.55784 / 0.33 (24147) hydrogen bonds : bond 0.04132 / 2.70 ( 936) hydrogen bonds : angle 3.47565 / 2.47 ( 2360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.09 seconds wall clock time: 48 minutes 47.89 seconds (2927.89 seconds total)