Starting phenix.real_space_refine on Fri Jul 3 20:17:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.cif Found real_map, /net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.map" model { file = "/net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7enn_31217/07_2026/7enn_31217.cif" } resolution = 2.8 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= 0.001 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: 7 Type Number sf(0) Gaussians P 294 5.49 5 S 31 5.16 5 Be 1 3.05 5 C 9365 2.51 5 N 2989 2.21 5 O 3636 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4315 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 14, 'TRANS': 524} Chain breaks: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.56, per 1000 atoms: 0.22 Number of scatterers: 16319 At special positions: 0 Unit cell: (143.431, 126.652, 115.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 31 16.00 P 294 15.00 F 3 9.00 O 3636 8.00 N 2989 7.00 C 9365 6.00 Be 1 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 513.7 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 63.5% alpha, 5.4% beta 145 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'K' and resid 32 through 40 removed outlier: 3.711A pdb=" N LEU K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 64 Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 103 through 105 No H-bonds generated for 'chain 'K' and resid 103 through 105' Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.576A pdb=" N GLN K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 138 Processing helix chain 'K' and resid 153 through 159 Processing helix chain 'K' and resid 161 through 165 Processing helix chain 'K' and resid 175 through 179 Processing helix chain 'K' and resid 184 through 192 removed outlier: 3.750A pdb=" N GLU K 192 " --> pdb=" O LYS K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 221 Processing helix chain 'K' and resid 226 through 228 No H-bonds generated for 'chain 'K' and resid 226 through 228' Processing helix chain 'K' and resid 229 through 237 removed outlier: 3.560A pdb=" N TYR K 237 " --> pdb=" O PHE K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 254 removed outlier: 3.867A pdb=" N GLU K 249 " --> pdb=" O GLU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 296 Processing helix chain 'K' and resid 313 through 324 removed outlier: 3.947A pdb=" N GLN K 317 " --> pdb=" O ASN K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 332 removed outlier: 4.781A pdb=" N ASP K 329 " --> pdb=" O TYR K 326 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY K 330 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL K 331 " --> pdb=" O PHE K 328 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU K 332 " --> pdb=" O ASP K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 363 Processing helix chain 'K' and resid 372 through 387 removed outlier: 3.511A pdb=" N LEU K 376 " --> pdb=" O MET K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 412 removed outlier: 3.943A pdb=" N HIS K 403 " --> pdb=" O GLY K 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY K 410 " --> pdb=" O ILE K 406 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN K 412 " --> pdb=" O ASN K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 425 Processing helix chain 'K' and resid 444 through 454 removed outlier: 4.237A pdb=" N ASP K 448 " --> pdb=" O ASN K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 488 removed outlier: 3.562A pdb=" N ILE K 478 " --> pdb=" O THR K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 498 removed outlier: 3.931A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 545 removed outlier: 3.964A pdb=" N SER K 540 " --> pdb=" O ILE K 536 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU K 542 " --> pdb=" O LEU K 538 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY K 543 " --> pdb=" O GLU K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 586 through 599 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.590A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.762A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.507A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.618A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.552A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.749A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.559A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.721A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.556A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.289A pdb=" N VAL K 124 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR K 152 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE K 98 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR K 151 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE K 100 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU K 99 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU K 171 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU K 201 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 173 " --> pdb=" O LEU K 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 390 through 393 removed outlier: 6.163A pdb=" N GLU K 391 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER K 420 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL K 393 " --> pdb=" O SER K 420 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL K 366 " --> pdb=" O PHE K 417 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU K 419 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU K 368 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL K 436 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU K 469 " --> pdb=" O VAL K 436 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE K 438 " --> pdb=" O LEU K 469 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY K 471 " --> pdb=" O PHE K 438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS K 280 " --> pdb=" O ILE K 470 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG A 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'L' and resid 96 through 98 removed outlier: 6.556A pdb=" N THR L 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.105A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.727A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.719A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.311A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 574 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3473 1.33 - 1.45: 4922 1.45 - 1.57: 8170 1.57 - 1.69: 586 1.69 - 1.81: 54 Bond restraints: 17205 Sorted by residual: bond pdb=" F2 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.705 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" F1 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.700 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" F3 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.690 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 ... (remaining 17200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 24440 4.21 - 8.42: 39 8.42 - 12.64: 3 12.64 - 16.85: 1 16.85 - 21.06: 1 Bond angle restraints: 24484 Sorted by residual: angle pdb=" F1 BEF K 902 " pdb="BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 120.12 99.06 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" F2 BEF K 902 " pdb="BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 119.96 105.13 14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 24479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 8134 35.15 - 70.31: 1435 70.31 - 105.46: 9 105.46 - 140.61: 3 140.61 - 175.77: 3 Dihedral angle restraints: 9584 sinusoidal: 5825 harmonic: 3759 Sorted by residual: dihedral pdb=" C5' ADP K 901 " pdb=" O5' ADP K 901 " pdb=" PA ADP K 901 " pdb=" O2A ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.77 -175.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PA ADP K 901 " pdb=" PB ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.01 -125.01 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PB ADP K 901 " pdb=" PA ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 58.31 -118.31 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 9581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1737 0.037 - 0.074: 741 0.074 - 0.111: 249 0.111 - 0.147: 40 0.147 - 0.184: 5 Chirality restraints: 2772 Sorted by residual: chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" C3' DA I 98 " pdb=" C4' DA I 98 " pdb=" O3' DA I 98 " pdb=" C2' DA I 98 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CB ILE H 91 " pdb=" CA ILE H 91 " pdb=" CG1 ILE H 91 " pdb=" CG2 ILE H 91 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2769 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 444 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO K 445 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 445 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 445 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 168 " 0.012 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP K 168 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP K 168 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP K 168 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 168 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 168 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 517 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE K 517 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE K 517 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU K 518 " 0.011 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 452 2.68 - 3.24: 14197 3.24 - 3.79: 28708 3.79 - 4.35: 38713 4.35 - 4.90: 56736 Nonbonded interactions: 138806 Sorted by model distance: nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.127 2.496 nonbonded pdb=" OH TYR K 153 " pdb=" O ASP K 174 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR K 214 " pdb=" O SER K 226 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.190 3.040 nonbonded pdb=" O SER K 244 " pdb=" OG SER K 248 " model vdw 2.205 3.040 ... (remaining 138801 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'F' and resid 23 through 101) selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.600 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 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 : 0.010 0.821 17208 Z= 0.927 Angle : 0.794 21.061 24484 Z= 0.642 Chirality : 0.045 0.184 2772 Planarity : 0.004 0.049 2097 Dihedral : 25.221 175.768 7160 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.16 (0.23), residues: 1274 helix: 1.02 (0.18), residues: 789 sheet: -0.83 (0.64), residues: 80 loop : -2.24 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 145 TYR 0.023 0.002 TYR G 50 PHE 0.015 0.002 PHE K 409 TRP 0.031 0.003 TRP K 168 HIS 0.003 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.54 (17205) covalent geometry : angle 0.79424 / 0.64 (24484) hydrogen bonds : bond 0.12383 / 7.78 ( 945) hydrogen bonds : angle 4.27816 / 3.00 ( 2418) Misc. bond : bond 0.57308 / 22.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.559 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.9740 time to fit residues: 214.5712 Evaluate side-chains 161 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.0040 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 429 ASN K 447 ASN K 488 GLN K 491 ASN L 93 GLN D 46 HIS F 93 GLN H 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090645 restraints weight = 23514.094| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.50 r_work: 0.3036 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17208 Z= 0.138 Angle : 0.645 9.485 24484 Z= 0.368 Chirality : 0.046 0.214 2772 Planarity : 0.004 0.040 2097 Dihedral : 29.055 170.296 4627 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.83 % Allowed : 9.70 % Favored : 88.47 % 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: 0.51 (0.24), residues: 1274 helix: 1.52 (0.18), residues: 790 sheet: -0.23 (0.68), residues: 75 loop : -1.98 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.013 0.001 TYR K 214 PHE 0.021 0.001 PHE K 409 TRP 0.012 0.001 TRP K 39 HIS 0.004 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (17205) covalent geometry : angle 0.64548 / 0.37 (24484) hydrogen bonds : bond 0.05171 / 3.51 ( 945) hydrogen bonds : angle 3.45113 / 2.44 ( 2418) Misc. bond : bond 0.00472 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7993 (tt0) cc_final: 0.7352 (mp0) REVERT: K 374 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8328 (mm-40) REVERT: K 398 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7490 (mmm160) REVERT: K 401 GLU cc_start: 0.8388 (mp0) cc_final: 0.8164 (mp0) REVERT: C 92 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: D 76 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8351 (ptp90) REVERT: H 105 LYS cc_start: 0.8512 (mtpm) cc_final: 0.8071 (mttp) outliers start: 20 outliers final: 6 residues processed: 192 average time/residue: 0.8967 time to fit residues: 185.2227 Evaluate side-chains 178 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 429 ASN K 488 GLN D 46 HIS D 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086823 restraints weight = 23630.474| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.48 r_work: 0.2962 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17208 Z= 0.240 Angle : 0.688 9.589 24484 Z= 0.382 Chirality : 0.049 0.221 2772 Planarity : 0.004 0.056 2097 Dihedral : 29.281 167.091 4627 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.47 % Allowed : 10.70 % Favored : 86.83 % 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: 0.58 (0.24), residues: 1274 helix: 1.59 (0.18), residues: 792 sheet: -0.48 (0.66), residues: 80 loop : -1.96 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 454 TYR 0.014 0.002 TYR L 51 PHE 0.029 0.002 PHE K 409 TRP 0.016 0.002 TRP K 39 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (17205) covalent geometry : angle 0.68783 / 0.38 (24484) hydrogen bonds : bond 0.06588 / 4.43 ( 945) hydrogen bonds : angle 3.39060 / 2.39 ( 2418) Misc. bond : bond 0.00904 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.517 Fit side-chains REVERT: K 275 GLU cc_start: 0.7998 (tt0) cc_final: 0.7387 (mp0) REVERT: K 374 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: K 401 GLU cc_start: 0.8438 (mp0) cc_final: 0.8211 (mp0) REVERT: C 92 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: D 44 GLN cc_start: 0.8925 (mt0) cc_final: 0.8645 (mt0) REVERT: D 76 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8463 (ptp90) REVERT: G 64 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8111 (tp30) outliers start: 27 outliers final: 12 residues processed: 183 average time/residue: 0.9076 time to fit residues: 178.4285 Evaluate side-chains 189 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088746 restraints weight = 23587.952| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.51 r_work: 0.2997 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17208 Z= 0.132 Angle : 0.636 9.344 24484 Z= 0.358 Chirality : 0.046 0.211 2772 Planarity : 0.004 0.036 2097 Dihedral : 29.272 163.339 4627 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.83 % Allowed : 12.26 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1274 helix: 1.82 (0.18), residues: 791 sheet: -0.30 (0.66), residues: 80 loop : -1.74 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.012 0.001 TYR F 51 PHE 0.021 0.001 PHE K 409 TRP 0.016 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (17205) covalent geometry : angle 0.63627 / 0.36 (24484) hydrogen bonds : bond 0.05096 / 3.46 ( 945) hydrogen bonds : angle 3.28458 / 2.32 ( 2418) Misc. bond : bond 0.00216 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.555 Fit side-chains REVERT: K 275 GLU cc_start: 0.7978 (tt0) cc_final: 0.7304 (mp0) REVERT: K 374 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: K 394 ASP cc_start: 0.8170 (t70) cc_final: 0.7853 (t0) REVERT: K 401 GLU cc_start: 0.8430 (mp0) cc_final: 0.8163 (mp0) REVERT: L 24 ASP cc_start: 0.8313 (t70) cc_final: 0.7961 (t0) REVERT: C 64 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: C 92 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: D 44 GLN cc_start: 0.8894 (mt0) cc_final: 0.8645 (mt0) REVERT: D 76 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8407 (ptp90) REVERT: D 90 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8261 (mp0) outliers start: 20 outliers final: 9 residues processed: 184 average time/residue: 0.8005 time to fit residues: 158.3077 Evaluate side-chains 189 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088282 restraints weight = 23413.971| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.50 r_work: 0.2950 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17208 Z= 0.167 Angle : 0.630 9.058 24484 Z= 0.354 Chirality : 0.046 0.206 2772 Planarity : 0.004 0.038 2097 Dihedral : 29.263 161.880 4627 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.92 % Allowed : 13.08 % Favored : 85.00 % 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: 1.05 (0.24), residues: 1274 helix: 1.92 (0.18), residues: 791 sheet: -0.22 (0.66), residues: 80 loop : -1.67 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.011 0.001 TYR F 51 PHE 0.021 0.001 PHE K 409 TRP 0.022 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (17205) covalent geometry : angle 0.63024 / 0.35 (24484) hydrogen bonds : bond 0.05328 / 3.61 ( 945) hydrogen bonds : angle 3.19527 / 2.26 ( 2418) Misc. bond : bond 0.00405 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.636 Fit side-chains REVERT: K 132 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: K 275 GLU cc_start: 0.7976 (tt0) cc_final: 0.7291 (mp0) REVERT: K 374 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8242 (mm-40) REVERT: K 401 GLU cc_start: 0.8474 (mp0) cc_final: 0.8206 (mp0) REVERT: C 64 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: C 92 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: D 76 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8429 (ptp90) outliers start: 21 outliers final: 10 residues processed: 179 average time/residue: 0.8281 time to fit residues: 159.5292 Evaluate side-chains 184 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 44 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.124019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.088643 restraints weight = 23463.590| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.49 r_work: 0.2954 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17208 Z= 0.164 Angle : 0.633 8.675 24484 Z= 0.355 Chirality : 0.045 0.210 2772 Planarity : 0.004 0.036 2097 Dihedral : 29.273 160.955 4627 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.92 % Allowed : 14.09 % Favored : 83.99 % 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: 1.16 (0.24), residues: 1274 helix: 2.00 (0.18), residues: 785 sheet: -0.22 (0.65), residues: 80 loop : -1.55 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.011 0.001 TYR L 51 PHE 0.018 0.001 PHE K 409 TRP 0.021 0.002 TRP K 39 HIS 0.003 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (17205) covalent geometry : angle 0.63295 / 0.35 (24484) hydrogen bonds : bond 0.05137 / 3.49 ( 945) hydrogen bonds : angle 3.16834 / 2.25 ( 2418) Misc. bond : bond 0.00208 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7970 (tt0) cc_final: 0.7287 (mp0) REVERT: K 374 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8273 (mm-40) REVERT: K 401 GLU cc_start: 0.8479 (mp0) cc_final: 0.8204 (mp0) REVERT: A 133 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: C 64 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: C 92 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: D 76 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8424 (ptp90) REVERT: G 64 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8049 (tp30) outliers start: 21 outliers final: 11 residues processed: 179 average time/residue: 0.9011 time to fit residues: 173.3247 Evaluate side-chains 184 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 131 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 114 optimal weight: 0.0170 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.124337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.088984 restraints weight = 23386.782| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.49 r_work: 0.2955 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17208 Z= 0.151 Angle : 0.630 8.548 24484 Z= 0.352 Chirality : 0.045 0.209 2772 Planarity : 0.004 0.036 2097 Dihedral : 29.265 160.480 4627 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.10 % Allowed : 14.09 % Favored : 83.81 % 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: 1.21 (0.24), residues: 1274 helix: 2.04 (0.18), residues: 785 sheet: -0.21 (0.65), residues: 80 loop : -1.52 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.011 0.001 TYR K 214 PHE 0.016 0.001 PHE K 409 TRP 0.018 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (17205) covalent geometry : angle 0.62966 / 0.35 (24484) hydrogen bonds : bond 0.05027 / 3.42 ( 945) hydrogen bonds : angle 3.15178 / 2.23 ( 2418) Misc. bond : bond 0.00195 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7967 (tt0) cc_final: 0.7289 (mp0) REVERT: K 401 GLU cc_start: 0.8464 (mp0) cc_final: 0.8182 (mp0) REVERT: A 133 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: C 64 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: C 92 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: D 76 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8431 (ptp90) REVERT: D 90 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: G 64 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: H 32 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (pt0) outliers start: 23 outliers final: 12 residues processed: 177 average time/residue: 0.8851 time to fit residues: 168.6978 Evaluate side-chains 188 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 122 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087374 restraints weight = 23391.992| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.48 r_work: 0.2968 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17208 Z= 0.218 Angle : 0.665 9.160 24484 Z= 0.367 Chirality : 0.047 0.217 2772 Planarity : 0.004 0.050 2097 Dihedral : 29.340 157.813 4627 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.47 % Allowed : 13.82 % Favored : 83.71 % 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: 1.07 (0.24), residues: 1274 helix: 1.93 (0.18), residues: 785 sheet: -0.24 (0.65), residues: 80 loop : -1.57 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.012 0.002 TYR F 51 PHE 0.020 0.002 PHE K 409 TRP 0.020 0.002 TRP K 39 HIS 0.003 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (17205) covalent geometry : angle 0.66467 / 0.37 (24484) hydrogen bonds : bond 0.05922 / 4.00 ( 945) hydrogen bonds : angle 3.19687 / 2.27 ( 2418) Misc. bond : bond 0.00246 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7978 (tt0) cc_final: 0.7328 (mp0) REVERT: K 374 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8265 (mm-40) REVERT: K 401 GLU cc_start: 0.8456 (mp0) cc_final: 0.8223 (mp0) REVERT: A 133 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: C 64 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8543 (tp30) REVERT: C 92 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: D 76 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8443 (ptp90) REVERT: E 59 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: G 64 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: H 32 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7912 (pt0) outliers start: 27 outliers final: 12 residues processed: 177 average time/residue: 0.8416 time to fit residues: 160.4916 Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 99 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088774 restraints weight = 23437.456| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.49 r_work: 0.2958 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17208 Z= 0.129 Angle : 0.635 9.360 24484 Z= 0.355 Chirality : 0.045 0.211 2772 Planarity : 0.004 0.042 2097 Dihedral : 29.310 155.057 4627 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 1.83 % Allowed : 14.91 % Favored : 83.26 % 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 (0.24), residues: 1274 helix: 2.05 (0.18), residues: 785 sheet: -0.21 (0.64), residues: 80 loop : -1.45 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 83 TYR 0.012 0.001 TYR K 214 PHE 0.025 0.001 PHE K 417 TRP 0.019 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (17205) covalent geometry : angle 0.63505 / 0.36 (24484) hydrogen bonds : bond 0.04900 / 3.34 ( 945) hydrogen bonds : angle 3.15593 / 2.24 ( 2418) Misc. bond : bond 0.00141 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7967 (tt0) cc_final: 0.7293 (mp0) REVERT: K 401 GLU cc_start: 0.8456 (mp0) cc_final: 0.8197 (mp0) REVERT: A 133 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: C 64 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: C 92 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: D 76 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8441 (ptp90) REVERT: E 59 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: F 93 GLN cc_start: 0.8459 (mt0) cc_final: 0.8252 (mm-40) REVERT: G 64 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: H 32 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7919 (pt0) outliers start: 20 outliers final: 10 residues processed: 180 average time/residue: 0.8797 time to fit residues: 170.2267 Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087130 restraints weight = 23341.420| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.48 r_work: 0.2966 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17208 Z= 0.227 Angle : 0.681 11.561 24484 Z= 0.372 Chirality : 0.047 0.215 2772 Planarity : 0.004 0.052 2097 Dihedral : 29.354 153.861 4627 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.92 % Allowed : 14.91 % Favored : 83.17 % 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: 1.08 (0.24), residues: 1274 helix: 1.92 (0.18), residues: 785 sheet: -0.25 (0.65), residues: 80 loop : -1.53 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 145 TYR 0.012 0.002 TYR F 51 PHE 0.023 0.002 PHE K 409 TRP 0.016 0.001 TRP K 39 HIS 0.003 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (17205) covalent geometry : angle 0.68092 / 0.37 (24484) hydrogen bonds : bond 0.05989 / 4.04 ( 945) hydrogen bonds : angle 3.20134 / 2.27 ( 2418) Misc. bond : bond 0.00242 / 0.10 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7976 (tt0) cc_final: 0.7330 (mp0) REVERT: K 401 GLU cc_start: 0.8459 (mp0) cc_final: 0.8231 (mp0) REVERT: A 133 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: C 64 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8551 (tp30) REVERT: C 92 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: D 76 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8464 (ptp90) REVERT: E 59 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: F 93 GLN cc_start: 0.8545 (mt0) cc_final: 0.8300 (mm-40) REVERT: G 64 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: H 32 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7942 (pt0) outliers start: 21 outliers final: 12 residues processed: 176 average time/residue: 0.8993 time to fit residues: 170.2452 Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088168 restraints weight = 23443.116| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.49 r_work: 0.2982 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17208 Z= 0.145 Angle : 0.659 14.415 24484 Z= 0.363 Chirality : 0.046 0.218 2772 Planarity : 0.004 0.040 2097 Dihedral : 29.345 154.381 4627 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.83 % Allowed : 15.65 % Favored : 82.53 % 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: 1.17 (0.24), residues: 1274 helix: 1.99 (0.18), residues: 785 sheet: -0.21 (0.65), residues: 80 loop : -1.49 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 145 TYR 0.012 0.001 TYR F 51 PHE 0.031 0.002 PHE K 417 TRP 0.016 0.001 TRP K 39 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (17205) covalent geometry : angle 0.65910 / 0.36 (24484) hydrogen bonds : bond 0.05322 / 3.61 ( 945) hydrogen bonds : angle 3.17273 / 2.25 ( 2418) Misc. bond : bond 0.00153 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6384.81 seconds wall clock time: 109 minutes 21.49 seconds (6561.49 seconds total)