Starting phenix.real_space_refine on Fri Jul 3 08:40:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwk_47253/07_2026/9dwk_47253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwk_47253/07_2026/9dwk_47253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwk_47253/07_2026/9dwk_47253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwk_47253/07_2026/9dwk_47253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwk_47253/07_2026/9dwk_47253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwk_47253/07_2026/9dwk_47253.map" } resolution = 4.3 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3861 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 249 5.49 5 C 5548 2.51 5 N 2015 2.21 5 O 2563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 10375 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 467 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 13, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 182 Chain: "B" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 392 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 11, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 516 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "E" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 477 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 13, 'TYR:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 187 Chain: "F" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 407 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ARG:plan': 12, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "G" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 501 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "H" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 455 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "I" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 2144 Classifications: {'DNA': 105} Link IDs: {'rna3p': 104} Chain: "J" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2579 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1593 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1047 Unresolved non-hydrogen angles: 1320 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASN:plan1': 12, 'ASP:plan': 21, 'GLU:plan': 26, 'PHE:plan': 14, 'GLN:plan1': 12, 'HIS:plan': 9, 'TYR:plan': 12, 'ARG:plan': 18, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 563 Time building chain proxies: 2.45, per 1000 atoms: 0.24 Number of scatterers: 10375 At special positions: 0 Unit cell: (101.258, 117.018, 149.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 249 15.00 O 2563 8.00 N 2015 7.00 C 5548 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: 1.13 Conformation dependent library (CDL) restraints added in 323.4 milliseconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 69.2% alpha, 4.7% beta 124 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.651A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.587A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.524A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.731A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.019A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 85 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.542A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.620A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.515A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.643A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.920A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'L' and resid 12 through 29 Processing helix chain 'L' and resid 32 through 49 removed outlier: 4.304A pdb=" N ALA L 38 " --> pdb=" O HIS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.578A pdb=" N LYS L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 80 Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 91 through 102 Processing helix chain 'L' and resid 107 through 117 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 133 through 142 Processing helix chain 'L' and resid 142 through 147 removed outlier: 3.547A pdb=" N GLU L 147 " --> pdb=" O PHE L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 209 through 221 Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.649A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 289 Processing helix chain 'L' and resid 315 through 323 Processing helix chain 'L' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.958A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.866A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.129A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.007A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.586A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'L' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'L' and resid 174 through 178 removed outlier: 4.829A pdb=" N ASP L 192 " --> pdb=" O CYS L 178 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET L 191 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG L 258 " --> pdb=" O MET L 191 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL L 193 " --> pdb=" O ARG L 258 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE L 260 " --> pdb=" O VAL L 193 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU L 195 " --> pdb=" O ILE L 260 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 291 through 293 536 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1317 1.29 - 1.38: 2613 1.38 - 1.46: 2305 1.46 - 1.54: 4171 1.54 - 1.62: 579 Bond restraints: 10985 Sorted by residual: bond pdb=" P DT K 108 " pdb=" OP3 DT K 108 " ideal model delta sigma weight residual 1.480 1.611 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C3' DG J 136 " pdb=" C2' DG J 136 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG I 22 " pdb=" C2' DG I 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C3' DC J 111 " pdb=" O3' DC J 111 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.49e+00 ... (remaining 10980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 14978 1.52 - 3.04: 1049 3.04 - 4.56: 79 4.56 - 6.08: 15 6.08 - 7.59: 15 Bond angle restraints: 16136 Sorted by residual: angle pdb=" O4' DA I 69 " pdb=" C4' DA I 69 " pdb=" C3' DA I 69 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" O4' DC I 80 " pdb=" C4' DC I 80 " pdb=" C3' DC I 80 " ideal model delta sigma weight residual 106.00 102.95 3.05 6.00e-01 2.78e+00 2.59e+01 angle pdb=" N3 DT K 115 " pdb=" C4 DT K 115 " pdb=" O4 DT K 115 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 27 " pdb=" C4 DT I 27 " pdb=" O4 DT I 27 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 16131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 4307 28.59 - 57.17: 1257 57.17 - 85.76: 164 85.76 - 114.34: 1 114.34 - 142.93: 2 Dihedral angle restraints: 5731 sinusoidal: 2681 harmonic: 3050 Sorted by residual: dihedral pdb=" C4' DG J 82 " pdb=" C3' DG J 82 " pdb=" O3' DG J 82 " pdb=" P DT J 83 " ideal model delta sinusoidal sigma weight residual 220.00 77.07 142.93 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 85.89 134.11 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1973 0.129 - 0.257: 8 0.257 - 0.385: 0 0.385 - 0.514: 1 0.514 - 0.642: 10 Chirality restraints: 1992 Sorted by residual: chirality pdb=" P DT I 2 " pdb=" OP1 DT I 2 " pdb=" OP2 DT I 2 " pdb=" O5' DT I 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DC K 116 " pdb=" OP1 DC K 116 " pdb=" OP2 DC K 116 " pdb=" O5' DC K 116 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.48e+00 chirality pdb=" P DC I 80 " pdb=" OP1 DC I 80 " pdb=" OP2 DC I 80 " pdb=" O5' DC I 80 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.67e+00 ... (remaining 1989 not shown) Planarity restraints: 1307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 80 " 0.027 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" N1 DC I 80 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC I 80 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 80 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC I 80 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 80 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 80 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DC I 80 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DC I 80 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.026 2.00e-02 2.50e+03 1.10e-02 3.30e+00 pdb=" N9 DA I 39 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.018 2.00e-02 2.50e+03 9.34e-03 2.18e+00 pdb=" N1 DT I 88 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.001 2.00e-02 2.50e+03 ... (remaining 1304 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1968 2.76 - 3.30: 9773 3.30 - 3.83: 21836 3.83 - 4.37: 21532 4.37 - 4.90: 30040 Nonbonded interactions: 85149 Sorted by model distance: nonbonded pdb=" O ARG E 83 " pdb=" N VAL F 81 " model vdw 2.231 3.120 nonbonded pdb=" N2 DG J 38 " pdb=" O2 DC K 110 " model vdw 2.310 2.496 nonbonded pdb=" N VAL A 117 " pdb=" OP2 DG I 71 " model vdw 2.319 3.120 nonbonded pdb=" O ARG A 83 " pdb=" N VAL B 81 " model vdw 2.340 3.120 nonbonded pdb=" N TYR E 41 " pdb=" OP1 DC I 84 " model vdw 2.355 3.120 ... (remaining 85144 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 41 through 133) selection = (chain 'E' and resid 41 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 19.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 1.050 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 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 : 0.006 0.131 10985 Z= 0.568 Angle : 0.805 7.594 16136 Z= 0.703 Chirality : 0.061 0.642 1992 Planarity : 0.003 0.014 1307 Dihedral : 30.863 142.931 3739 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.01 (0.26), residues: 1048 helix: 1.83 (0.19), residues: 717 sheet: 2.21 (0.93), residues: 29 loop : 0.13 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.57 (10985) covalent geometry : angle 0.80464 / 0.70 (16136) hydrogen bonds : bond 0.12123 / 9.19 ( 857) hydrogen bonds : angle 4.39653 / 3.40 ( 2219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0481 time to fit residues: 1.8442 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.024279 restraints weight = 147878.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.024768 restraints weight = 94404.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.025103 restraints weight = 69604.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.025333 restraints weight = 56535.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.025438 restraints weight = 49624.594| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 10985 Z= 0.145 Angle : 0.576 8.222 16136 Z= 0.361 Chirality : 0.045 0.227 1992 Planarity : 0.002 0.012 1307 Dihedral : 30.952 145.366 3739 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.86 (0.26), residues: 1048 helix: 2.56 (0.19), residues: 731 sheet: 2.28 (0.92), residues: 29 loop : 0.11 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.14 (10985) covalent geometry : angle 0.57642 / 0.36 (16136) hydrogen bonds : bond 0.04497 / 3.40 ( 857) hydrogen bonds : angle 3.33649 / 2.61 ( 2219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0458 time to fit residues: 1.7103 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 113 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 23 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.021846 restraints weight = 159404.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.022461 restraints weight = 90086.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.022900 restraints weight = 61593.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.023203 restraints weight = 47444.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.023412 restraints weight = 39525.167| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10985 Z= 0.283 Angle : 0.685 9.228 16136 Z= 0.423 Chirality : 0.047 0.272 1992 Planarity : 0.003 0.013 1307 Dihedral : 31.175 147.366 3739 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.63 (0.26), residues: 1048 helix: 2.32 (0.19), residues: 730 sheet: 2.01 (0.88), residues: 29 loop : 0.27 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.28 (10985) covalent geometry : angle 0.68537 / 0.42 (16136) hydrogen bonds : bond 0.09633 / 7.34 ( 857) hydrogen bonds : angle 3.87147 / 3.01 ( 2219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.290 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0465 time to fit residues: 1.7713 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 3 optimal weight: 0.0870 chunk 98 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 overall best weight: 2.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.040054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.022782 restraints weight = 156072.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.023452 restraints weight = 86791.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.023927 restraints weight = 58392.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.024263 restraints weight = 44504.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.024462 restraints weight = 36955.816| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 10985 Z= 0.140 Angle : 0.561 7.556 16136 Z= 0.352 Chirality : 0.044 0.249 1992 Planarity : 0.002 0.012 1307 Dihedral : 31.138 145.538 3739 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 3.65 (0.27), residues: 1048 helix: 3.21 (0.20), residues: 731 sheet: 1.82 (0.89), residues: 29 loop : 0.33 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.14 (10985) covalent geometry : angle 0.56109 / 0.35 (16136) hydrogen bonds : bond 0.04029 / 3.05 ( 857) hydrogen bonds : angle 3.09914 / 2.41 ( 2219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0457 time to fit residues: 1.6834 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 40.0000 chunk 67 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 101 optimal weight: 100.0000 chunk 2 optimal weight: 40.0000 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 98 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.022629 restraints weight = 155670.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.023285 restraints weight = 87005.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.023742 restraints weight = 58868.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.024061 restraints weight = 45163.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.024289 restraints weight = 37742.132| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 10985 Z= 0.156 Angle : 0.568 7.432 16136 Z= 0.353 Chirality : 0.043 0.241 1992 Planarity : 0.002 0.012 1307 Dihedral : 31.079 146.458 3739 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 3.73 (0.27), residues: 1048 helix: 3.27 (0.19), residues: 731 sheet: 1.78 (0.89), residues: 29 loop : 0.36 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.16 (10985) covalent geometry : angle 0.56824 / 0.35 (16136) hydrogen bonds : bond 0.05291 / 4.02 ( 857) hydrogen bonds : angle 3.08840 / 2.40 ( 2219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0347 time to fit residues: 1.3767 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 94 optimal weight: 50.0000 chunk 46 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.0060 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.040574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.023242 restraints weight = 155547.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.023940 restraints weight = 86150.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.024433 restraints weight = 57810.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.024790 restraints weight = 43931.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.024987 restraints weight = 36277.711| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 10985 Z= 0.119 Angle : 0.536 7.548 16136 Z= 0.335 Chirality : 0.043 0.239 1992 Planarity : 0.002 0.011 1307 Dihedral : 30.929 145.490 3739 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 4.22 (0.27), residues: 1048 helix: 3.68 (0.19), residues: 731 sheet: 1.70 (0.87), residues: 29 loop : 0.46 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00135 / 0.12 (10985) covalent geometry : angle 0.53561 / 0.34 (16136) hydrogen bonds : bond 0.03464 / 2.60 ( 857) hydrogen bonds : angle 2.70303 / 2.10 ( 2219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.290 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0322 time to fit residues: 1.2902 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 6.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.039176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.022269 restraints weight = 157639.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.022897 restraints weight = 88229.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.023356 restraints weight = 60230.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.023669 restraints weight = 46102.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.023888 restraints weight = 38401.791| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 10985 Z= 0.208 Angle : 0.601 7.654 16136 Z= 0.368 Chirality : 0.044 0.251 1992 Planarity : 0.003 0.013 1307 Dihedral : 31.071 146.982 3739 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 3.80 (0.27), residues: 1048 helix: 3.33 (0.19), residues: 731 sheet: 1.63 (0.87), residues: 29 loop : 0.38 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.21 (10985) covalent geometry : angle 0.60119 / 0.37 (16136) hydrogen bonds : bond 0.07460 / 5.68 ( 857) hydrogen bonds : angle 3.22540 / 2.50 ( 2219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0368 time to fit residues: 1.4779 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 50.0000 chunk 23 optimal weight: 30.0000 chunk 68 optimal weight: 40.0000 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 94 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 overall best weight: 12.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.020919 restraints weight = 162519.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.021474 restraints weight = 93026.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.021862 restraints weight = 64160.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.022109 restraints weight = 49870.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.022318 restraints weight = 42167.839| |-----------------------------------------------------------------------------| r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10985 Z= 0.340 Angle : 0.760 11.225 16136 Z= 0.458 Chirality : 0.050 0.290 1992 Planarity : 0.004 0.025 1307 Dihedral : 31.543 149.024 3739 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.82 (0.25), residues: 1048 helix: 1.81 (0.18), residues: 720 sheet: 0.92 (0.92), residues: 29 loop : -0.16 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.34 (10985) covalent geometry : angle 0.76011 / 0.46 (16136) hydrogen bonds : bond 0.11989 / 9.14 ( 857) hydrogen bonds : angle 4.48039 / 3.48 ( 2219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0475 time to fit residues: 1.7691 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 50.0000 chunk 103 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.022722 restraints weight = 151622.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.023177 restraints weight = 95216.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.023461 restraints weight = 69786.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.023682 restraints weight = 57311.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.023798 restraints weight = 50410.599| |-----------------------------------------------------------------------------| r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 10985 Z= 0.168 Angle : 0.599 8.207 16136 Z= 0.369 Chirality : 0.045 0.258 1992 Planarity : 0.002 0.013 1307 Dihedral : 31.515 146.572 3739 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 3.24 (0.27), residues: 1048 helix: 2.96 (0.19), residues: 738 sheet: 1.37 (0.99), residues: 23 loop : -0.02 (0.40), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.17 (10985) covalent geometry : angle 0.59861 / 0.37 (16136) hydrogen bonds : bond 0.05191 / 3.95 ( 857) hydrogen bonds : angle 3.40010 / 2.64 ( 2219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0469 time to fit residues: 1.8088 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 98 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 93 optimal weight: 40.0000 chunk 124 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 overall best weight: 16.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.037263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.021366 restraints weight = 158414.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.021752 restraints weight = 103721.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.022000 restraints weight = 78331.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.022160 restraints weight = 65223.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.022233 restraints weight = 58244.560| |-----------------------------------------------------------------------------| r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 10985 Z= 0.420 Angle : 0.816 11.690 16136 Z= 0.488 Chirality : 0.053 0.294 1992 Planarity : 0.004 0.015 1307 Dihedral : 31.706 148.640 3739 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 27.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.46 (0.25), residues: 1048 helix: 1.53 (0.18), residues: 717 sheet: 0.55 (0.92), residues: 29 loop : -0.24 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.42 (10985) covalent geometry : angle 0.81556 / 0.49 (16136) hydrogen bonds : bond 0.13269 / 10.11 ( 857) hydrogen bonds : angle 4.85331 / 3.77 ( 2219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.298 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0468 time to fit residues: 1.7870 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 103 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 87 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.038434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.022175 restraints weight = 152813.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.022608 restraints weight = 95797.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.022872 restraints weight = 70470.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.023085 restraints weight = 58033.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.023196 restraints weight = 51124.458| |-----------------------------------------------------------------------------| r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 10985 Z= 0.208 Angle : 0.634 8.815 16136 Z= 0.388 Chirality : 0.046 0.259 1992 Planarity : 0.003 0.013 1307 Dihedral : 31.822 146.844 3739 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.51 (0.26), residues: 1048 helix: 2.43 (0.19), residues: 741 sheet: 0.93 (1.03), residues: 23 loop : -0.37 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.21 (10985) covalent geometry : angle 0.63378 / 0.39 (16136) hydrogen bonds : bond 0.06189 / 4.72 ( 857) hydrogen bonds : angle 3.78140 / 2.94 ( 2219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4671.15 seconds wall clock time: 79 minutes 59.27 seconds (4799.27 seconds total)