Starting phenix.real_space_refine on Fri Sep 19 00:01:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihe_52866/09_2025/9ihe_52866.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihe_52866/09_2025/9ihe_52866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ihe_52866/09_2025/9ihe_52866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihe_52866/09_2025/9ihe_52866.map" model { file = "/net/cci-nas-00/data/ceres_data/9ihe_52866/09_2025/9ihe_52866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihe_52866/09_2025/9ihe_52866.cif" } resolution = 2.95 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 290 5.49 5 S 70 5.16 5 C 12368 2.51 5 N 3902 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21069 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.90, per 1000 atoms: 0.23 Number of scatterers: 21069 At special positions: 0 Unit cell: (119.68, 120.36, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 70 16.00 P 290 15.00 O 4437 8.00 N 3902 7.00 C 12368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 440 " - pdb=" SG CYS L 497 " distance=2.04 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 564 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 696.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 19 sheets defined 56.0% alpha, 3.0% beta 134 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.097A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.565A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.546A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.792A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.062A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.502A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.704A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) 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: 3.563A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.541A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.524A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.827A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (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 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.670A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 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 removed outlier: 3.738A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.804A pdb=" N GLN K 75 " --> pdb=" O PRO K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 98 Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.649A pdb=" N TYR L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY L 178 " --> pdb=" O SER L 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 173 through 178' Processing helix chain 'L' and resid 180 through 188 removed outlier: 3.594A pdb=" N ARG L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 225 removed outlier: 3.805A pdb=" N ASN L 225 " --> pdb=" O CYS L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 268 Processing helix chain 'L' and resid 272 through 302 removed outlier: 5.362A pdb=" N LEU L 297 " --> pdb=" O TYR L 293 " (cutoff:3.500A) Proline residue: L 298 - end of helix Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 327 through 332 Processing helix chain 'L' and resid 333 through 338 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 368 through 373 removed outlier: 3.667A pdb=" N VAL L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 416 through 428 Processing helix chain 'L' and resid 432 through 441 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 458 through 469 Processing helix chain 'L' and resid 470 through 474 removed outlier: 3.536A pdb=" N ILE L 474 " --> pdb=" O PRO L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 483 Processing helix chain 'L' and resid 492 through 510 removed outlier: 3.505A pdb=" N ASP L 510 " --> pdb=" O LEU L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 540 Processing helix chain 'L' and resid 571 through 576 removed outlier: 4.271A pdb=" N SER L 574 " --> pdb=" O ASN L 571 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG L 576 " --> pdb=" O ALA L 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 219 through 225 removed outlier: 4.242A pdb=" N LEU N 223 " --> pdb=" O ASP N 219 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 302 removed outlier: 5.353A pdb=" N LEU N 297 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Proline residue: N 298 - end of helix Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 327 through 332 Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.578A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 399 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 441 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.556A pdb=" N ALA N 461 " --> pdb=" O ASN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 Processing helix chain 'N' and resid 571 through 576 removed outlier: 4.248A pdb=" N SER N 574 " --> pdb=" O ASN N 571 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG N 576 " --> pdb=" O ALA N 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.959A 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 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.117A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.667A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.083A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.162A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.631A pdb=" N ARG K 27 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 78 through 83 removed outlier: 4.368A pdb=" N ALA L 389 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'L' and resid 342 through 344 Processing sheet with id=AB5, first strand: chain 'L' and resid 546 through 547 Processing sheet with id=AB6, first strand: chain 'M' and resid 27 through 28 removed outlier: 3.522A pdb=" N ARG M 27 " --> pdb=" O ASN N 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.130A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 188 through 189 removed outlier: 4.568A pdb=" N LEU N 196 " --> pdb=" O ASN N 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AC1, first strand: chain 'N' and resid 546 through 547 702 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 8167 1.38 - 1.55: 13230 1.55 - 1.72: 584 1.72 - 1.88: 116 1.88 - 2.05: 8 Bond restraints: 22105 Sorted by residual: bond pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C3' DA J -22 " pdb=" O3' DA J -22 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" C3' DA J 32 " pdb=" O3' DA J 32 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CG ARG M 17 " pdb=" CD ARG M 17 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG N 349 " pdb=" CD ARG N 349 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 22100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 30364 1.49 - 2.99: 724 2.99 - 4.48: 74 4.48 - 5.98: 24 5.98 - 7.47: 5 Bond angle restraints: 31191 Sorted by residual: angle pdb=" CB ARG M 17 " pdb=" CG ARG M 17 " pdb=" CD ARG M 17 " ideal model delta sigma weight residual 111.30 118.77 -7.47 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CB ARG L 270 " pdb=" CG ARG L 270 " pdb=" CD ARG L 270 " ideal model delta sigma weight residual 111.30 118.27 -6.97 2.30e+00 1.89e-01 9.18e+00 angle pdb=" N ASN L 157 " pdb=" CA ASN L 157 " pdb=" C ASN L 157 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.48e+00 angle pdb=" CG ARG N 349 " pdb=" CD ARG N 349 " pdb=" NE ARG N 349 " ideal model delta sigma weight residual 112.00 117.53 -5.53 2.20e+00 2.07e-01 6.31e+00 angle pdb=" C PRO L 132 " pdb=" N ASN L 133 " pdb=" CA ASN L 133 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.20e+00 ... (remaining 31186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 10987 35.02 - 70.04: 1668 70.04 - 105.06: 26 105.06 - 140.08: 2 140.08 - 175.10: 6 Dihedral angle restraints: 12689 sinusoidal: 7261 harmonic: 5428 Sorted by residual: dihedral pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " pdb=" O3' DA J 32 " pdb=" P DC J 33 " ideal model delta sinusoidal sigma weight residual 220.00 44.90 175.10 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA J -31 " pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " pdb=" P DG J -30 " ideal model delta sinusoidal sigma weight residual 220.00 60.63 159.37 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DC J 35 " pdb=" C3' DC J 35 " pdb=" O3' DC J 35 " pdb=" P DC J 36 " ideal model delta sinusoidal sigma weight residual 220.00 62.75 157.25 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 12686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2083 0.029 - 0.057: 983 0.057 - 0.086: 252 0.086 - 0.115: 118 0.115 - 0.143: 23 Chirality restraints: 3459 Sorted by residual: chirality pdb=" CA ASN N 133 " pdb=" N ASN N 133 " pdb=" C ASN N 133 " pdb=" CB ASN N 133 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" P DC J 36 " pdb=" OP1 DC J 36 " pdb=" OP2 DC J 36 " pdb=" O5' DC J 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE H 86 " pdb=" N ILE H 86 " pdb=" C ILE H 86 " pdb=" CB ILE H 86 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 3456 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 109 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C SER D 109 " -0.032 2.00e-02 2.50e+03 pdb=" O SER D 109 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU D 110 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 110 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU H 110 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU H 110 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY H 111 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 108 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C VAL H 108 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL H 108 " -0.011 2.00e-02 2.50e+03 pdb=" N SER H 109 " -0.010 2.00e-02 2.50e+03 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 555 2.68 - 3.24: 18180 3.24 - 3.79: 35862 3.79 - 4.35: 49080 4.35 - 4.90: 74610 Nonbonded interactions: 178287 Sorted by model distance: nonbonded pdb=" OD2 ASP C 90 " pdb=" NH2 ARG L 307 " model vdw 2.129 3.120 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG N 307 " model vdw 2.164 3.120 nonbonded pdb=" OH TYR L 350 " pdb=" O THR L 545 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.246 3.040 ... (remaining 178282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.770 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.008 0.644 22112 Z= 0.206 Angle : 0.557 7.469 31201 Z= 0.313 Chirality : 0.037 0.143 3459 Planarity : 0.005 0.055 3007 Dihedral : 24.940 175.095 9164 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.43 % Allowed : 25.40 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.02 (0.19), residues: 1846 helix: 1.59 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.24 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 349 TYR 0.010 0.001 TYR L 177 PHE 0.010 0.001 PHE K 86 TRP 0.007 0.001 TRP M 89 HIS 0.002 0.001 HIS L 250 Details of bonding type rmsd covalent geometry : bond 0.00478 (22105) covalent geometry : angle 0.55658 (31191) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.60935 ( 10) hydrogen bonds : bond 0.12574 ( 1046) hydrogen bonds : angle 5.07056 ( 2730) Misc. bond : bond 0.64040 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8398 (t0) cc_final: 0.7817 (t0) REVERT: D 56 MET cc_start: 0.8775 (tpp) cc_final: 0.8539 (mmm) REVERT: E 56 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8553 (mtmm) REVERT: E 79 LYS cc_start: 0.8804 (tttm) cc_final: 0.8594 (tttt) REVERT: E 122 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7677 (pttt) REVERT: F 93 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7813 (mm-40) REVERT: G 15 LYS cc_start: 0.8643 (mttt) cc_final: 0.8149 (mtpt) REVERT: G 95 LYS cc_start: 0.8759 (tttt) cc_final: 0.8266 (ttmt) REVERT: G 99 ARG cc_start: 0.8652 (mtp180) cc_final: 0.7809 (mmm160) REVERT: G 108 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8562 (mp) REVERT: H 68 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: K 7 TYR cc_start: 0.8613 (m-80) cc_final: 0.8274 (m-80) REVERT: K 56 PHE cc_start: 0.8355 (m-80) cc_final: 0.8053 (m-80) REVERT: L 216 LEU cc_start: 0.7561 (mt) cc_final: 0.7210 (mp) REVERT: L 229 ARG cc_start: 0.7919 (tmm160) cc_final: 0.7651 (tmm160) REVERT: M 67 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: N 205 ASP cc_start: 0.7647 (t0) cc_final: 0.7250 (t0) REVERT: N 530 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8438 (mm110) outliers start: 23 outliers final: 15 residues processed: 204 average time/residue: 0.9037 time to fit residues: 202.7181 Evaluate side-chains 200 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 530 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 60 ASN K 80 GLN K 88 GLN L 122 GLN L 133 ASN M 54 ASN M 75 GLN N 133 ASN N 140 GLN N 257 HIS N 330 ASN N 421 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093094 restraints weight = 26869.916| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.61 r_work: 0.2926 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.257 22112 Z= 0.161 Angle : 0.542 12.466 31201 Z= 0.298 Chirality : 0.036 0.139 3459 Planarity : 0.004 0.038 3007 Dihedral : 27.033 176.216 5442 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.61 % Allowed : 22.17 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.34 (0.20), residues: 1846 helix: 1.85 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -0.22 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 42 TYR 0.011 0.001 TYR L 177 PHE 0.008 0.001 PHE K 86 TRP 0.009 0.001 TRP N 436 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00372 (22105) covalent geometry : angle 0.54199 (31191) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.75977 ( 10) hydrogen bonds : bond 0.04672 ( 1046) hydrogen bonds : angle 3.66581 ( 2730) Misc. bond : bond 0.25500 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8148 (mtm) REVERT: C 73 ASN cc_start: 0.7900 (t0) cc_final: 0.7371 (t0) REVERT: E 56 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8541 (mtmm) REVERT: E 79 LYS cc_start: 0.8828 (tttm) cc_final: 0.8540 (tttt) REVERT: E 122 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7671 (pttt) REVERT: G 15 LYS cc_start: 0.8269 (mttt) cc_final: 0.7691 (mtpt) REVERT: G 95 LYS cc_start: 0.8817 (tttt) cc_final: 0.8348 (ttmt) REVERT: G 99 ARG cc_start: 0.8538 (mtp180) cc_final: 0.7847 (mmm160) REVERT: H 32 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: K 7 TYR cc_start: 0.8619 (m-80) cc_final: 0.8115 (m-80) REVERT: K 56 PHE cc_start: 0.8139 (m-80) cc_final: 0.7808 (m-80) REVERT: L 216 LEU cc_start: 0.7453 (mt) cc_final: 0.7065 (mp) REVERT: L 229 ARG cc_start: 0.7934 (tmm160) cc_final: 0.7659 (tmm160) REVERT: L 271 TRP cc_start: 0.6711 (OUTLIER) cc_final: 0.6445 (m-10) REVERT: M 81 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: N 205 ASP cc_start: 0.7574 (t0) cc_final: 0.7151 (t0) REVERT: N 349 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8049 (ttm110) outliers start: 58 outliers final: 18 residues processed: 229 average time/residue: 0.8754 time to fit residues: 221.0863 Evaluate side-chains 207 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 271 TRP Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 567 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 177 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 122 GLN L 133 ASN M 54 ASN M 75 GLN M 88 GLN N 133 ASN N 140 GLN N 330 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.091584 restraints weight = 26919.897| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.61 r_work: 0.2898 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.210 22112 Z= 0.200 Angle : 0.552 12.579 31201 Z= 0.303 Chirality : 0.038 0.135 3459 Planarity : 0.004 0.037 3007 Dihedral : 27.042 175.530 5415 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.05 % Allowed : 22.54 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.33 (0.20), residues: 1846 helix: 1.86 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.25 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 70 TYR 0.019 0.001 TYR L 177 PHE 0.009 0.001 PHE H 62 TRP 0.007 0.001 TRP N 436 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00477 (22105) covalent geometry : angle 0.55204 (31191) SS BOND : bond 0.00418 ( 5) SS BOND : angle 0.68347 ( 10) hydrogen bonds : bond 0.05024 ( 1046) hydrogen bonds : angle 3.59156 ( 2730) Misc. bond : bond 0.20623 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: C 73 ASN cc_start: 0.7897 (t0) cc_final: 0.7446 (t160) REVERT: E 79 LYS cc_start: 0.8860 (tttm) cc_final: 0.8636 (tttt) REVERT: E 122 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7723 (pttt) REVERT: F 93 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7860 (mm-40) REVERT: G 15 LYS cc_start: 0.8301 (mttt) cc_final: 0.7711 (mtpt) REVERT: G 95 LYS cc_start: 0.8818 (tttt) cc_final: 0.8351 (ttmt) REVERT: G 99 ARG cc_start: 0.8540 (mtp180) cc_final: 0.7833 (mmm160) REVERT: H 68 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: K 7 TYR cc_start: 0.8658 (m-80) cc_final: 0.8170 (m-80) REVERT: K 56 PHE cc_start: 0.8156 (m-80) cc_final: 0.7839 (m-80) REVERT: L 216 LEU cc_start: 0.7515 (mt) cc_final: 0.7127 (mp) REVERT: L 229 ARG cc_start: 0.7956 (tmm160) cc_final: 0.7676 (tmm160) REVERT: L 250 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7869 (m90) REVERT: L 556 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7420 (t) REVERT: N 205 ASP cc_start: 0.7535 (t0) cc_final: 0.7129 (t0) REVERT: N 349 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7989 (ttm110) REVERT: N 411 MET cc_start: 0.8173 (mtp) cc_final: 0.7819 (OUTLIER) outliers start: 65 outliers final: 26 residues processed: 235 average time/residue: 0.8193 time to fit residues: 213.7906 Evaluate side-chains 219 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 177 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 133 ASN M 75 GLN N 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093326 restraints weight = 26830.021| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.61 r_work: 0.2928 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 22112 Z= 0.152 Angle : 0.526 11.262 31201 Z= 0.291 Chirality : 0.036 0.142 3459 Planarity : 0.004 0.037 3007 Dihedral : 26.960 176.802 5415 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.93 % Allowed : 23.66 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.50 (0.20), residues: 1846 helix: 2.01 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.19 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 42 TYR 0.012 0.001 TYR L 177 PHE 0.008 0.001 PHE K 86 TRP 0.008 0.001 TRP N 436 HIS 0.003 0.000 HIS L 257 Details of bonding type rmsd covalent geometry : bond 0.00352 (22105) covalent geometry : angle 0.52579 (31191) SS BOND : bond 0.00400 ( 5) SS BOND : angle 0.72130 ( 10) hydrogen bonds : bond 0.04425 ( 1046) hydrogen bonds : angle 3.46279 ( 2730) Misc. bond : bond 0.18752 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8125 (mtm) REVERT: C 73 ASN cc_start: 0.7803 (t0) cc_final: 0.7383 (t0) REVERT: E 79 LYS cc_start: 0.8810 (tttm) cc_final: 0.8521 (tttt) REVERT: E 122 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7671 (pttt) REVERT: G 15 LYS cc_start: 0.8251 (mttt) cc_final: 0.7676 (mtpt) REVERT: G 95 LYS cc_start: 0.8815 (tttt) cc_final: 0.8340 (ttmt) REVERT: G 99 ARG cc_start: 0.8531 (mtp180) cc_final: 0.7830 (mmm160) REVERT: G 108 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8453 (mp) REVERT: H 68 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: K 7 TYR cc_start: 0.8640 (m-80) cc_final: 0.8138 (m-80) REVERT: K 56 PHE cc_start: 0.8164 (m-80) cc_final: 0.7851 (m-80) REVERT: L 216 LEU cc_start: 0.7524 (mt) cc_final: 0.7121 (mp) REVERT: L 556 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7401 (t) REVERT: M 27 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8041 (mtt-85) REVERT: M 81 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8260 (mm-30) REVERT: N 205 ASP cc_start: 0.7564 (t0) cc_final: 0.7098 (t0) REVERT: N 349 ARG cc_start: 0.8228 (mmp-170) cc_final: 0.7990 (ttm110) REVERT: N 504 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7447 (ttm110) REVERT: N 564 CYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7966 (p) outliers start: 47 outliers final: 21 residues processed: 224 average time/residue: 0.7736 time to fit residues: 191.5829 Evaluate side-chains 213 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN N 330 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094047 restraints weight = 26779.968| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.61 r_work: 0.2942 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 22112 Z= 0.146 Angle : 0.518 10.240 31201 Z= 0.286 Chirality : 0.036 0.142 3459 Planarity : 0.004 0.041 3007 Dihedral : 26.841 177.579 5414 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.11 % Allowed : 23.85 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.64 (0.20), residues: 1846 helix: 2.13 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.13 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 70 TYR 0.015 0.001 TYR L 177 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP N 436 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00337 (22105) covalent geometry : angle 0.51838 (31191) SS BOND : bond 0.00389 ( 5) SS BOND : angle 0.61258 ( 10) hydrogen bonds : bond 0.04193 ( 1046) hydrogen bonds : angle 3.36301 ( 2730) Misc. bond : bond 0.17260 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8107 (mtm) REVERT: C 73 ASN cc_start: 0.7760 (t0) cc_final: 0.7408 (t0) REVERT: C 92 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8250 (mp0) REVERT: E 79 LYS cc_start: 0.8821 (tttm) cc_final: 0.8525 (tttt) REVERT: E 122 LYS cc_start: 0.8176 (ptmt) cc_final: 0.7659 (pttt) REVERT: G 15 LYS cc_start: 0.8207 (mttt) cc_final: 0.7655 (mtpt) REVERT: G 95 LYS cc_start: 0.8811 (tttt) cc_final: 0.8332 (ttmt) REVERT: G 99 ARG cc_start: 0.8517 (mtp180) cc_final: 0.7824 (mmm160) REVERT: G 108 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8454 (mp) REVERT: H 32 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: H 68 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: K 7 TYR cc_start: 0.8630 (m-80) cc_final: 0.8131 (m-80) REVERT: K 56 PHE cc_start: 0.8161 (m-80) cc_final: 0.7855 (m-80) REVERT: L 216 LEU cc_start: 0.7466 (mt) cc_final: 0.7050 (mp) REVERT: M 27 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8054 (mtt-85) REVERT: N 205 ASP cc_start: 0.7568 (t0) cc_final: 0.7099 (t0) REVERT: N 349 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7945 (ttm110) REVERT: N 504 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7437 (ttp-170) REVERT: N 564 CYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7914 (p) outliers start: 50 outliers final: 26 residues processed: 226 average time/residue: 0.8203 time to fit residues: 205.4729 Evaluate side-chains 219 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN K 80 GLN L 133 ASN M 75 GLN M 88 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.090032 restraints weight = 26743.482| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.61 r_work: 0.2889 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.177 22112 Z= 0.261 Angle : 0.586 13.361 31201 Z= 0.318 Chirality : 0.040 0.135 3459 Planarity : 0.004 0.042 3007 Dihedral : 27.037 175.003 5410 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.48 % Allowed : 22.42 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.30 (0.20), residues: 1846 helix: 1.86 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.29 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 70 TYR 0.013 0.001 TYR L 177 PHE 0.012 0.001 PHE H 62 TRP 0.006 0.001 TRP K 89 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00628 (22105) covalent geometry : angle 0.58633 (31191) SS BOND : bond 0.00309 ( 5) SS BOND : angle 0.78702 ( 10) hydrogen bonds : bond 0.05516 ( 1046) hydrogen bonds : angle 3.55975 ( 2730) Misc. bond : bond 0.17359 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 190 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: C 73 ASN cc_start: 0.7873 (t0) cc_final: 0.7488 (t0) REVERT: C 92 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: C 104 GLN cc_start: 0.8695 (mm110) cc_final: 0.8431 (mm-40) REVERT: D 120 SER cc_start: 0.8531 (m) cc_final: 0.8259 (p) REVERT: E 79 LYS cc_start: 0.8835 (tttm) cc_final: 0.8616 (tttt) REVERT: E 122 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7717 (pttt) REVERT: G 15 LYS cc_start: 0.8334 (mttt) cc_final: 0.7729 (mtpt) REVERT: G 95 LYS cc_start: 0.8810 (tttt) cc_final: 0.8339 (ttmt) REVERT: G 99 ARG cc_start: 0.8540 (mtp180) cc_final: 0.7806 (mmm160) REVERT: G 108 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8496 (mp) REVERT: H 68 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: K 7 TYR cc_start: 0.8676 (m-80) cc_final: 0.8177 (m-80) REVERT: K 56 PHE cc_start: 0.8160 (m-80) cc_final: 0.7843 (m-80) REVERT: L 216 LEU cc_start: 0.7528 (mt) cc_final: 0.7106 (mp) REVERT: L 250 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.7888 (m90) REVERT: L 556 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7371 (t) REVERT: L 571 ASN cc_start: 0.8016 (t0) cc_final: 0.7624 (t0) REVERT: N 185 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7565 (mtm-85) REVERT: N 205 ASP cc_start: 0.7533 (t0) cc_final: 0.7112 (t0) REVERT: N 404 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: N 504 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7428 (ttm110) REVERT: N 564 CYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7875 (p) outliers start: 72 outliers final: 33 residues processed: 242 average time/residue: 0.8247 time to fit residues: 221.2945 Evaluate side-chains 228 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 404 GLU Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 105 optimal weight: 0.0050 chunk 203 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.092185 restraints weight = 26829.338| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.72 r_work: 0.2890 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 22112 Z= 0.159 Angle : 0.550 11.217 31201 Z= 0.303 Chirality : 0.037 0.143 3459 Planarity : 0.004 0.078 3007 Dihedral : 27.031 175.737 5409 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.05 % Allowed : 23.47 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.44 (0.20), residues: 1846 helix: 1.97 (0.17), residues: 991 sheet: None (None), residues: 0 loop : -0.23 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 349 TYR 0.013 0.001 TYR L 177 PHE 0.009 0.001 PHE A 67 TRP 0.009 0.001 TRP K 89 HIS 0.003 0.001 HIS L 257 Details of bonding type rmsd covalent geometry : bond 0.00369 (22105) covalent geometry : angle 0.55040 (31191) SS BOND : bond 0.00259 ( 5) SS BOND : angle 0.69257 ( 10) hydrogen bonds : bond 0.04793 ( 1046) hydrogen bonds : angle 3.47587 ( 2730) Misc. bond : bond 0.18767 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: C 73 ASN cc_start: 0.7827 (t0) cc_final: 0.7441 (t0) REVERT: C 92 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8239 (mp0) REVERT: D 120 SER cc_start: 0.8499 (m) cc_final: 0.8216 (p) REVERT: E 79 LYS cc_start: 0.8850 (tttm) cc_final: 0.8632 (tttt) REVERT: E 122 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7718 (pttt) REVERT: G 15 LYS cc_start: 0.8322 (mttt) cc_final: 0.7744 (mtpt) REVERT: G 95 LYS cc_start: 0.8827 (tttt) cc_final: 0.8357 (ttmt) REVERT: G 99 ARG cc_start: 0.8555 (mtp180) cc_final: 0.7842 (mmm160) REVERT: G 108 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8492 (mp) REVERT: H 68 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: K 7 TYR cc_start: 0.8670 (m-80) cc_final: 0.8178 (m-80) REVERT: K 56 PHE cc_start: 0.8172 (m-80) cc_final: 0.7851 (m-80) REVERT: L 216 LEU cc_start: 0.7529 (mt) cc_final: 0.7149 (mp) REVERT: L 250 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.7954 (m90) REVERT: L 571 ASN cc_start: 0.7998 (t0) cc_final: 0.7634 (t0) REVERT: M 27 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8049 (mtt-85) REVERT: N 205 ASP cc_start: 0.7567 (t0) cc_final: 0.7164 (t0) REVERT: N 504 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7484 (ttp-170) REVERT: N 564 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7863 (p) outliers start: 49 outliers final: 30 residues processed: 223 average time/residue: 0.8549 time to fit residues: 210.2584 Evaluate side-chains 223 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 196 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.092474 restraints weight = 26750.214| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.61 r_work: 0.2913 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 22112 Z= 0.176 Angle : 0.545 11.203 31201 Z= 0.298 Chirality : 0.037 0.138 3459 Planarity : 0.004 0.041 3007 Dihedral : 26.957 176.706 5409 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.18 % Allowed : 23.35 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.49 (0.20), residues: 1846 helix: 2.01 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.20 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 42 TYR 0.014 0.001 TYR L 177 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP K 89 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00416 (22105) covalent geometry : angle 0.54477 (31191) SS BOND : bond 0.00299 ( 5) SS BOND : angle 0.69616 ( 10) hydrogen bonds : bond 0.04633 ( 1046) hydrogen bonds : angle 3.43412 ( 2730) Misc. bond : bond 0.17033 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8146 (mtm) REVERT: C 73 ASN cc_start: 0.7839 (t0) cc_final: 0.7471 (t0) REVERT: C 92 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8233 (mp0) REVERT: D 56 MET cc_start: 0.8855 (tpp) cc_final: 0.8591 (mmm) REVERT: D 120 SER cc_start: 0.8463 (m) cc_final: 0.8198 (p) REVERT: E 79 LYS cc_start: 0.8848 (tttm) cc_final: 0.8632 (tttt) REVERT: E 122 LYS cc_start: 0.8214 (ptmt) cc_final: 0.7703 (pttt) REVERT: G 15 LYS cc_start: 0.8300 (mttt) cc_final: 0.7723 (mtpt) REVERT: G 95 LYS cc_start: 0.8823 (tttt) cc_final: 0.8352 (ttmt) REVERT: G 99 ARG cc_start: 0.8537 (mtp180) cc_final: 0.7837 (mmm160) REVERT: G 108 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8481 (mp) REVERT: H 68 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: K 7 TYR cc_start: 0.8662 (m-80) cc_final: 0.8185 (m-80) REVERT: K 56 PHE cc_start: 0.8153 (m-80) cc_final: 0.7835 (m-80) REVERT: L 216 LEU cc_start: 0.7577 (mt) cc_final: 0.7151 (mp) REVERT: L 229 ARG cc_start: 0.7842 (tmm160) cc_final: 0.7479 (tmm160) REVERT: L 250 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.7831 (m90) REVERT: L 556 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7419 (t) REVERT: L 571 ASN cc_start: 0.8007 (t0) cc_final: 0.7634 (t0) REVERT: M 27 ARG cc_start: 0.8456 (mtp85) cc_final: 0.7874 (mtp-110) REVERT: N 205 ASP cc_start: 0.7546 (t0) cc_final: 0.7141 (t0) REVERT: N 411 MET cc_start: 0.8026 (mtp) cc_final: 0.7794 (ptp) REVERT: N 504 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7460 (ttm110) outliers start: 51 outliers final: 31 residues processed: 226 average time/residue: 0.8529 time to fit residues: 213.1040 Evaluate side-chains 220 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 504 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 84 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 192 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN L 133 ASN L 526 GLN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.092601 restraints weight = 26707.120| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.61 r_work: 0.2917 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 22112 Z= 0.165 Angle : 0.541 10.196 31201 Z= 0.298 Chirality : 0.037 0.141 3459 Planarity : 0.004 0.044 3007 Dihedral : 26.950 176.748 5409 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.68 % Allowed : 23.79 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.51 (0.20), residues: 1846 helix: 2.01 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.18 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 70 TYR 0.014 0.001 TYR L 177 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP K 89 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00385 (22105) covalent geometry : angle 0.54126 (31191) SS BOND : bond 0.00282 ( 5) SS BOND : angle 0.85109 ( 10) hydrogen bonds : bond 0.04548 ( 1046) hydrogen bonds : angle 3.44171 ( 2730) Misc. bond : bond 0.17605 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8133 (mtm) REVERT: C 73 ASN cc_start: 0.7831 (t0) cc_final: 0.7464 (t0) REVERT: C 92 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: D 56 MET cc_start: 0.8845 (tpp) cc_final: 0.8578 (mmm) REVERT: D 120 SER cc_start: 0.8460 (m) cc_final: 0.8198 (p) REVERT: E 79 LYS cc_start: 0.8843 (tttm) cc_final: 0.8558 (tttt) REVERT: E 122 LYS cc_start: 0.8210 (ptmt) cc_final: 0.7694 (pttt) REVERT: G 15 LYS cc_start: 0.8292 (mttt) cc_final: 0.7718 (mtpt) REVERT: G 95 LYS cc_start: 0.8823 (tttt) cc_final: 0.8353 (ttmt) REVERT: G 99 ARG cc_start: 0.8536 (mtp180) cc_final: 0.7834 (mmm160) REVERT: G 108 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8476 (mp) REVERT: H 68 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: K 7 TYR cc_start: 0.8658 (m-80) cc_final: 0.8182 (m-80) REVERT: K 56 PHE cc_start: 0.8151 (m-80) cc_final: 0.7833 (m-80) REVERT: L 216 LEU cc_start: 0.7555 (mt) cc_final: 0.7132 (mp) REVERT: L 250 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7819 (m90) REVERT: L 571 ASN cc_start: 0.8007 (t0) cc_final: 0.7647 (t0) REVERT: M 27 ARG cc_start: 0.8431 (mtp85) cc_final: 0.7871 (mtp-110) REVERT: N 205 ASP cc_start: 0.7552 (t0) cc_final: 0.7149 (t0) REVERT: N 404 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: N 411 MET cc_start: 0.8050 (mtp) cc_final: 0.7797 (ptp) REVERT: N 504 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7456 (ttm110) outliers start: 43 outliers final: 30 residues processed: 216 average time/residue: 0.8572 time to fit residues: 204.6583 Evaluate side-chains 223 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 404 GLU Chi-restraints excluded: chain N residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 149 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092866 restraints weight = 26811.111| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.61 r_work: 0.2920 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 22112 Z= 0.153 Angle : 0.547 10.038 31201 Z= 0.299 Chirality : 0.037 0.305 3459 Planarity : 0.004 0.043 3007 Dihedral : 26.943 176.775 5409 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.55 % Allowed : 23.97 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 1.54 (0.20), residues: 1846 helix: 2.04 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.16 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 576 TYR 0.013 0.001 TYR L 177 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP K 89 HIS 0.002 0.000 HIS L 257 Details of bonding type rmsd covalent geometry : bond 0.00354 (22105) covalent geometry : angle 0.54719 (31191) SS BOND : bond 0.00280 ( 5) SS BOND : angle 0.71004 ( 10) hydrogen bonds : bond 0.04445 ( 1046) hydrogen bonds : angle 3.44912 ( 2730) Misc. bond : bond 0.17569 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: C 73 ASN cc_start: 0.7823 (t0) cc_final: 0.7456 (t0) REVERT: C 92 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: D 56 MET cc_start: 0.8836 (tpp) cc_final: 0.8568 (mmm) REVERT: D 120 SER cc_start: 0.8453 (m) cc_final: 0.8190 (p) REVERT: E 79 LYS cc_start: 0.8837 (tttm) cc_final: 0.8550 (tttt) REVERT: E 122 LYS cc_start: 0.8188 (ptmt) cc_final: 0.7676 (pttt) REVERT: G 15 LYS cc_start: 0.8284 (mttt) cc_final: 0.7705 (mtpt) REVERT: G 95 LYS cc_start: 0.8820 (tttt) cc_final: 0.8348 (ttmt) REVERT: G 99 ARG cc_start: 0.8534 (mtp180) cc_final: 0.7831 (mmm160) REVERT: G 108 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8472 (mp) REVERT: H 68 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: K 7 TYR cc_start: 0.8655 (m-80) cc_final: 0.8178 (m-80) REVERT: K 56 PHE cc_start: 0.8150 (m-80) cc_final: 0.7837 (m-80) REVERT: L 216 LEU cc_start: 0.7553 (mt) cc_final: 0.7128 (mp) REVERT: L 250 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7817 (m90) REVERT: L 270 ARG cc_start: 0.7577 (ptm-80) cc_final: 0.7330 (ptm-80) REVERT: L 556 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7425 (t) REVERT: L 571 ASN cc_start: 0.8002 (t0) cc_final: 0.7643 (t0) REVERT: M 27 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7857 (mtp-110) REVERT: N 205 ASP cc_start: 0.7551 (t0) cc_final: 0.7149 (t0) REVERT: N 404 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: N 411 MET cc_start: 0.8067 (mtp) cc_final: 0.7837 (ptp) REVERT: N 504 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7445 (ttm110) outliers start: 41 outliers final: 31 residues processed: 213 average time/residue: 0.8264 time to fit residues: 193.6304 Evaluate side-chains 224 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 133 ASN Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 404 GLU Chi-restraints excluded: chain N residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 29 optimal weight: 0.7980 chunk 153 optimal weight: 0.0970 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093003 restraints weight = 26846.788| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.61 r_work: 0.2920 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 22112 Z= 0.218 Angle : 0.714 59.198 31201 Z= 0.414 Chirality : 0.038 0.511 3459 Planarity : 0.004 0.060 3007 Dihedral : 26.953 176.789 5409 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.06 % Favored : 97.89 % Rotamer: Outliers : 2.62 % Allowed : 23.85 % Favored : 73.54 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.55 (0.20), residues: 1846 helix: 2.04 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.15 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 70 TYR 0.011 0.001 TYR L 177 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP K 89 HIS 0.003 0.000 HIS L 257 Details of bonding type rmsd covalent geometry : bond 0.00425 (22105) covalent geometry : angle 0.71438 (31191) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.67554 ( 10) hydrogen bonds : bond 0.04439 ( 1046) hydrogen bonds : angle 3.44975 ( 2730) Misc. bond : bond 0.17560 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7767.71 seconds wall clock time: 132 minutes 46.52 seconds (7966.52 seconds total)