Starting phenix.real_space_refine on Sat Aug 23 17:05:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjp_41307/08_2025/8tjp_41307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjp_41307/08_2025/8tjp_41307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tjp_41307/08_2025/8tjp_41307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjp_41307/08_2025/8tjp_41307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tjp_41307/08_2025/8tjp_41307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjp_41307/08_2025/8tjp_41307.map" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8340 2.51 5 N 2484 2.21 5 O 2604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13464 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 bond proxies already assigned to first conformer: 6728 Chain: "B" Number of atoms: 6732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 bond proxies already assigned to first conformer: 6728 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 13 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG A 13 " occ=0.52 residue: pdb=" N AARG A 27 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG A 27 " occ=0.39 residue: pdb=" N AASN A 48 " occ=0.47 ... (14 atoms not shown) pdb=" ND2BASN A 48 " occ=0.53 residue: pdb=" N AARG A 58 " occ=0.29 ... (20 atoms not shown) pdb=" NH2BARG A 58 " occ=0.71 residue: pdb=" N AGLU A 161 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 161 " occ=0.54 residue: pdb=" N AARG A 486 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG A 486 " occ=0.55 residue: pdb=" N AARG B 13 " occ=0.58 ... (20 atoms not shown) pdb=" NH2BARG B 13 " occ=0.42 residue: pdb=" N AARG B 27 " occ=0.42 ... (20 atoms not shown) pdb=" NH2BARG B 27 " occ=0.58 residue: pdb=" N AASN B 48 " occ=0.51 ... (14 atoms not shown) pdb=" ND2BASN B 48 " occ=0.49 residue: pdb=" N AARG B 58 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.56 residue: pdb=" N AGLU B 161 " occ=0.70 ... (16 atoms not shown) pdb=" OE2BGLU B 161 " occ=0.30 residue: pdb=" N AARG B 486 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG B 486 " occ=0.43 Time building chain proxies: 5.71, per 1000 atoms: 0.42 Number of scatterers: 13464 At special positions: 0 Unit cell: (114.466, 96.492, 199.606, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2604 8.00 N 2484 7.00 C 8340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 48.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 removed outlier: 3.723A pdb=" N ASP A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.221A pdb=" N VAL A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.807A pdb=" N SER A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.550A pdb=" N VAL A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.889A pdb=" N CYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.525A pdb=" N VAL A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.869A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 481 through 498 removed outlier: 3.877A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 527 through 541 Processing helix chain 'A' and resid 575 through 582 removed outlier: 4.067A pdb=" N SER A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 596 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'A' and resid 603 through 610 removed outlier: 3.505A pdb=" N VAL A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 641 removed outlier: 3.844A pdb=" N GLN A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Proline residue: A 625 - end of helix removed outlier: 3.648A pdb=" N TYR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 663 removed outlier: 3.749A pdb=" N ALA A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.718A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.543A pdb=" N ARG A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 770 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 810 through 821 Processing helix chain 'A' and resid 835 through 845 Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'B' and resid 3 through 32 removed outlier: 3.776A pdb=" N ASP B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.539A pdb=" N ARG B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 178 through 191 removed outlier: 4.000A pdb=" N SER B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.521A pdb=" N GLN B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.662A pdb=" N CYS B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.512A pdb=" N VAL B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.443A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 379 through 382 removed outlier: 3.578A pdb=" N ALA B 382 " --> pdb=" O THR B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 481 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 527 through 541 Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.801A pdb=" N SER B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 619 through 641 Proline residue: B 625 - end of helix Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.774A pdb=" N ALA B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 683 Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'B' and resid 727 through 740 Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.723A pdb=" N ARG B 761 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 Processing helix chain 'B' and resid 792 through 796 Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 883 through 888 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 8.454A pdb=" N ILE A 197 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 150 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 199 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 152 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 230 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A 38 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU A 276 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE A 36 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 290 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 293 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 453 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 295 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS A 451 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 297 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN A 449 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 334 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU A 367 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.521A pdb=" N GLN A 427 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 479 Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 removed outlier: 5.172A pdb=" N GLY A 650 " --> pdb=" O HIS A 783 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 647 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 561 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 689 through 692 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199 removed outlier: 8.319A pdb=" N ILE B 197 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL B 150 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 199 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 230 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 274 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER B 38 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU B 276 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE B 36 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 290 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 453 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B 295 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS B 451 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 297 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN B 449 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 334 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 441 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA9, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 479 Processing sheet with id=AB2, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.761A pdb=" N ARG B 789 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 650 " --> pdb=" O HIS B 783 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 560 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 649 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 562 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 561 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 689 through 692 681 hydrogen bonds defined for protein. 1922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4808 1.34 - 1.46: 2821 1.46 - 1.58: 6033 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 13724 Sorted by residual: bond pdb=" N VAL A 643 " pdb=" CA VAL A 643 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.23e+00 bond pdb=" C ILE B 376 " pdb=" O ILE B 376 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.19e+00 bond pdb=" CB VAL B 174 " pdb=" CG2 VAL B 174 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB PRO A 86 " pdb=" CG PRO A 86 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" C GLY A 95 " pdb=" O GLY A 95 " ideal model delta sigma weight residual 1.231 1.242 -0.011 1.11e-02 8.12e+03 1.06e+00 ... (remaining 13719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 18162 1.54 - 3.07: 416 3.07 - 4.61: 75 4.61 - 6.14: 14 6.14 - 7.68: 5 Bond angle restraints: 18672 Sorted by residual: angle pdb=" CB AASN A 48 " pdb=" CG AASN A 48 " pdb=" ND2AASN A 48 " ideal model delta sigma weight residual 116.40 124.08 -7.68 1.50e+00 4.44e-01 2.62e+01 angle pdb=" CB BASN B 48 " pdb=" CG BASN B 48 " pdb=" ND2BASN B 48 " ideal model delta sigma weight residual 116.40 124.06 -7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" CB BASN A 48 " pdb=" CG BASN A 48 " pdb=" ND2BASN A 48 " ideal model delta sigma weight residual 116.40 123.97 -7.57 1.50e+00 4.44e-01 2.54e+01 angle pdb=" CB AASN B 48 " pdb=" CG AASN B 48 " pdb=" ND2AASN B 48 " ideal model delta sigma weight residual 116.40 123.96 -7.56 1.50e+00 4.44e-01 2.54e+01 angle pdb=" N TYR A 752 " pdb=" CA TYR A 752 " pdb=" C TYR A 752 " ideal model delta sigma weight residual 107.88 112.91 -5.03 1.41e+00 5.03e-01 1.27e+01 ... (remaining 18667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 7541 16.87 - 33.75: 519 33.75 - 50.62: 122 50.62 - 67.50: 28 67.50 - 84.37: 18 Dihedral angle restraints: 8228 sinusoidal: 3150 harmonic: 5078 Sorted by residual: dihedral pdb=" CA CYS B 41 " pdb=" C CYS B 41 " pdb=" N ARG B 42 " pdb=" CA ARG B 42 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA PHE B 264 " pdb=" C PHE B 264 " pdb=" N GLY B 265 " pdb=" CA GLY B 265 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG A 430 " pdb=" CD ARG A 430 " pdb=" NE ARG A 430 " pdb=" CZ ARG A 430 " ideal model delta sinusoidal sigma weight residual 180.00 137.32 42.68 2 1.50e+01 4.44e-03 9.80e+00 ... (remaining 8225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1298 0.028 - 0.057: 517 0.057 - 0.085: 139 0.085 - 0.114: 99 0.114 - 0.142: 37 Chirality restraints: 2090 Sorted by residual: chirality pdb=" CA VAL A 548 " pdb=" N VAL A 548 " pdb=" C VAL A 548 " pdb=" CB VAL A 548 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL A 226 " pdb=" N VAL A 226 " pdb=" C VAL A 226 " pdb=" CB VAL A 226 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2087 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 582 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO B 583 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 85 " -0.036 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 86 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 328 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 329 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " -0.027 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 411 2.71 - 3.26: 13970 3.26 - 3.80: 21132 3.80 - 4.35: 26019 4.35 - 4.90: 45138 Nonbonded interactions: 106670 Sorted by model distance: nonbonded pdb=" N GLU B 820 " pdb=" OE1 GLU B 820 " model vdw 2.161 3.120 nonbonded pdb=" O ARG A 460 " pdb=" NH1 ARG A 460 " model vdw 2.170 3.120 nonbonded pdb=" NE2 GLN A 122 " pdb=" O GLY A 176 " model vdw 2.281 3.120 nonbonded pdb=" O ASP A 139 " pdb=" OG SER A 142 " model vdw 2.292 3.040 nonbonded pdb=" O ARG B 498 " pdb=" NH1 ARG B 528 " model vdw 2.300 3.120 ... (remaining 106665 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 910)) selection = (chain 'B' and (resid 2 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 910)) } 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=0.29 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.003 0.052 13724 Z= 0.147 Angle : 0.604 7.681 18672 Z= 0.347 Chirality : 0.040 0.142 2090 Planarity : 0.005 0.056 2520 Dihedral : 13.180 84.371 4984 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 0.73 % Allowed : 7.04 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1812 helix: 2.05 (0.20), residues: 722 sheet: 0.10 (0.34), residues: 226 loop : -0.91 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 244 TYR 0.010 0.001 TYR B 823 PHE 0.011 0.001 PHE B 103 TRP 0.012 0.001 TRP B 602 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00294 (13724) covalent geometry : angle 0.60447 (18672) hydrogen bonds : bond 0.17117 ( 681) hydrogen bonds : angle 5.87775 ( 1922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.335 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0941 time to fit residues: 6.9143 Evaluate side-chains 34 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.028435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.020426 restraints weight = 890456.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.021662 restraints weight = 171341.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.022590 restraints weight = 85497.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.023222 restraints weight = 54770.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.023692 restraints weight = 39846.820| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13724 Z= 0.124 Angle : 0.576 8.536 18672 Z= 0.295 Chirality : 0.043 0.156 2090 Planarity : 0.005 0.050 2520 Dihedral : 3.809 21.191 1994 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.03 % Allowed : 6.82 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1812 helix: 2.43 (0.19), residues: 742 sheet: 0.61 (0.35), residues: 228 loop : -0.54 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 359 TYR 0.010 0.001 TYR B 800 PHE 0.015 0.001 PHE A 242 TRP 0.013 0.001 TRP A 801 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00273 (13724) covalent geometry : angle 0.57644 (18672) hydrogen bonds : bond 0.03806 ( 681) hydrogen bonds : angle 4.34647 ( 1922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8703 (ptm) cc_final: 0.8209 (ptm) REVERT: A 596 MET cc_start: 0.9555 (mtp) cc_final: 0.9333 (mtp) REVERT: A 681 MET cc_start: 0.9154 (tpt) cc_final: 0.8779 (tpt) REVERT: A 690 MET cc_start: 0.8486 (mtt) cc_final: 0.8035 (mpp) REVERT: B 224 MET cc_start: 0.9705 (mmm) cc_final: 0.9438 (mmm) REVERT: B 681 MET cc_start: 0.9495 (tpp) cc_final: 0.9265 (tpp) outliers start: 6 outliers final: 0 residues processed: 42 average time/residue: 0.0909 time to fit residues: 6.8744 Evaluate side-chains 33 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 86 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 600 GLN A 624 GLN A 902 GLN B 51 GLN B 397 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.025401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.017970 restraints weight = 839045.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.019103 restraints weight = 172367.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.019929 restraints weight = 87131.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.020513 restraints weight = 56400.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.020911 restraints weight = 41456.129| |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13724 Z= 0.355 Angle : 0.790 13.018 18672 Z= 0.397 Chirality : 0.044 0.151 2090 Planarity : 0.006 0.052 2520 Dihedral : 4.451 21.980 1994 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.25 % Allowed : 7.11 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1812 helix: 1.70 (0.18), residues: 766 sheet: 0.23 (0.32), residues: 236 loop : -0.66 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 705 TYR 0.015 0.002 TYR B 906 PHE 0.014 0.002 PHE B 157 TRP 0.017 0.002 TRP A 602 HIS 0.010 0.002 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00744 (13724) covalent geometry : angle 0.78957 (18672) hydrogen bonds : bond 0.04826 ( 681) hydrogen bonds : angle 4.87958 ( 1922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8790 (ptm) cc_final: 0.8575 (ptm) REVERT: A 596 MET cc_start: 0.9555 (mtp) cc_final: 0.9230 (mtp) REVERT: A 681 MET cc_start: 0.9165 (tpt) cc_final: 0.8790 (tpt) REVERT: B 224 MET cc_start: 0.9664 (mmm) cc_final: 0.9392 (mmm) REVERT: B 681 MET cc_start: 0.9522 (tpp) cc_final: 0.9210 (tpt) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 0.0957 time to fit residues: 6.6013 Evaluate side-chains 33 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 20 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 902 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.026470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.019018 restraints weight = 892175.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.020169 restraints weight = 168994.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.021028 restraints weight = 84320.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.021623 restraints weight = 54002.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.022054 restraints weight = 39444.745| |-----------------------------------------------------------------------------| r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2463 r_free = 0.2463 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2463 r_free = 0.2463 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13724 Z= 0.134 Angle : 0.568 14.725 18672 Z= 0.285 Chirality : 0.042 0.150 2090 Planarity : 0.004 0.049 2520 Dihedral : 3.917 18.714 1994 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.88 % Allowed : 7.26 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.20), residues: 1812 helix: 2.20 (0.19), residues: 766 sheet: 0.52 (0.34), residues: 234 loop : -0.47 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 359 TYR 0.010 0.001 TYR A 802 PHE 0.011 0.001 PHE A 585 TRP 0.013 0.001 TRP A 801 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00290 (13724) covalent geometry : angle 0.56797 (18672) hydrogen bonds : bond 0.03542 ( 681) hydrogen bonds : angle 4.19650 ( 1922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 596 MET cc_start: 0.9540 (mtp) cc_final: 0.9269 (mtp) REVERT: A 681 MET cc_start: 0.9179 (tpt) cc_final: 0.8780 (tpt) REVERT: A 872 MET cc_start: 0.9253 (mtm) cc_final: 0.8887 (ptp) REVERT: B 224 MET cc_start: 0.9692 (mmm) cc_final: 0.9424 (mmm) REVERT: B 599 MET cc_start: 0.9377 (mmm) cc_final: 0.9125 (mmm) REVERT: B 681 MET cc_start: 0.9503 (tpp) cc_final: 0.9234 (tpt) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.0977 time to fit residues: 5.4572 Evaluate side-chains 31 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS B 804 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.027163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.019593 restraints weight = 876030.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.020768 restraints weight = 166896.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.021656 restraints weight = 83145.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.022254 restraints weight = 53061.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.022701 restraints weight = 38944.237| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13724 Z= 0.093 Angle : 0.526 11.954 18672 Z= 0.262 Chirality : 0.041 0.138 2090 Planarity : 0.004 0.049 2520 Dihedral : 3.591 17.498 1994 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 6.89 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.20), residues: 1812 helix: 2.55 (0.19), residues: 754 sheet: 0.80 (0.35), residues: 226 loop : -0.25 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 732 TYR 0.007 0.001 TYR B 11 PHE 0.013 0.001 PHE A 585 TRP 0.012 0.001 TRP B 54 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00207 (13724) covalent geometry : angle 0.52632 (18672) hydrogen bonds : bond 0.03072 ( 681) hydrogen bonds : angle 3.91113 ( 1922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.510 Fit side-chains REVERT: A 681 MET cc_start: 0.9201 (tpt) cc_final: 0.8814 (tpt) REVERT: B 224 MET cc_start: 0.9688 (mmm) cc_final: 0.9469 (mmm) REVERT: B 631 MET cc_start: 0.9347 (mtp) cc_final: 0.9087 (ttt) REVERT: B 681 MET cc_start: 0.9496 (tpp) cc_final: 0.9231 (tpt) outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 0.0855 time to fit residues: 5.1785 Evaluate side-chains 32 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN A 783 HIS B 567 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.027250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.019690 restraints weight = 885722.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.020881 restraints weight = 167457.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.021776 restraints weight = 83173.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.022389 restraints weight = 52894.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.022833 restraints weight = 38457.282| |-----------------------------------------------------------------------------| r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13724 Z= 0.095 Angle : 0.517 11.177 18672 Z= 0.257 Chirality : 0.040 0.140 2090 Planarity : 0.004 0.048 2520 Dihedral : 3.464 17.621 1994 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.10 % Allowed : 6.74 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.20), residues: 1812 helix: 2.55 (0.19), residues: 768 sheet: 0.79 (0.34), residues: 232 loop : -0.28 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.009 0.001 TYR B 641 PHE 0.012 0.001 PHE A 585 TRP 0.011 0.001 TRP A 801 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00212 (13724) covalent geometry : angle 0.51693 (18672) hydrogen bonds : bond 0.03003 ( 681) hydrogen bonds : angle 3.84854 ( 1922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.582 Fit side-chains REVERT: A 681 MET cc_start: 0.9217 (tpt) cc_final: 0.8871 (tpp) REVERT: B 224 MET cc_start: 0.9692 (mmm) cc_final: 0.9468 (mmm) REVERT: B 599 MET cc_start: 0.9097 (mmm) cc_final: 0.8835 (mmm) REVERT: B 681 MET cc_start: 0.9488 (tpp) cc_final: 0.9209 (tpt) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.0969 time to fit residues: 5.9103 Evaluate side-chains 34 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 606 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.026739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.019221 restraints weight = 897584.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.020396 restraints weight = 170645.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.021265 restraints weight = 84801.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.021860 restraints weight = 54333.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.022290 restraints weight = 39848.279| |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13724 Z= 0.129 Angle : 0.540 10.392 18672 Z= 0.268 Chirality : 0.040 0.179 2090 Planarity : 0.004 0.046 2520 Dihedral : 3.495 16.899 1994 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.03 % Allowed : 7.11 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.20), residues: 1812 helix: 2.58 (0.19), residues: 768 sheet: 0.74 (0.34), residues: 232 loop : -0.29 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 817 TYR 0.009 0.001 TYR B 641 PHE 0.011 0.001 PHE A 585 TRP 0.011 0.001 TRP A 801 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00285 (13724) covalent geometry : angle 0.53999 (18672) hydrogen bonds : bond 0.03152 ( 681) hydrogen bonds : angle 3.90416 ( 1922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.464 Fit side-chains REVERT: A 681 MET cc_start: 0.9197 (tpt) cc_final: 0.8907 (tpp) REVERT: B 224 MET cc_start: 0.9687 (mmm) cc_final: 0.9429 (mmm) REVERT: B 599 MET cc_start: 0.9117 (mmm) cc_final: 0.8872 (mmm) REVERT: B 681 MET cc_start: 0.9496 (tpp) cc_final: 0.9210 (tpt) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.1048 time to fit residues: 6.1133 Evaluate side-chains 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 631 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.027183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.019624 restraints weight = 859241.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.020818 restraints weight = 167091.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.021707 restraints weight = 83457.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.022317 restraints weight = 53220.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.022758 restraints weight = 38706.435| |-----------------------------------------------------------------------------| r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13724 Z= 0.090 Angle : 0.517 10.363 18672 Z= 0.256 Chirality : 0.040 0.189 2090 Planarity : 0.004 0.048 2520 Dihedral : 3.363 17.260 1994 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 1.10 % Allowed : 6.96 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.20), residues: 1812 helix: 2.62 (0.19), residues: 766 sheet: 0.80 (0.34), residues: 232 loop : -0.28 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.008 0.001 TYR B 641 PHE 0.016 0.001 PHE A 868 TRP 0.011 0.001 TRP A 54 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00202 (13724) covalent geometry : angle 0.51732 (18672) hydrogen bonds : bond 0.02901 ( 681) hydrogen bonds : angle 3.79433 ( 1922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.520 Fit side-chains REVERT: A 681 MET cc_start: 0.9210 (tpt) cc_final: 0.8883 (tpp) REVERT: B 224 MET cc_start: 0.9689 (mmm) cc_final: 0.9425 (mmm) REVERT: B 599 MET cc_start: 0.9101 (mmm) cc_final: 0.8844 (mmm) REVERT: B 681 MET cc_start: 0.9443 (tpp) cc_final: 0.9199 (tpp) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.1038 time to fit residues: 6.0789 Evaluate side-chains 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 50 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.027047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.019458 restraints weight = 930562.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.020642 restraints weight = 171905.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021514 restraints weight = 85225.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.022130 restraints weight = 54927.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.022568 restraints weight = 40029.700| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13724 Z= 0.098 Angle : 0.515 10.159 18672 Z= 0.255 Chirality : 0.040 0.171 2090 Planarity : 0.004 0.049 2520 Dihedral : 3.317 17.279 1994 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 1.10 % Allowed : 6.96 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.20), residues: 1812 helix: 2.65 (0.19), residues: 768 sheet: 0.82 (0.34), residues: 232 loop : -0.27 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.009 0.001 TYR B 641 PHE 0.012 0.001 PHE A 585 TRP 0.010 0.001 TRP A 801 HIS 0.002 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00220 (13724) covalent geometry : angle 0.51468 (18672) hydrogen bonds : bond 0.02923 ( 681) hydrogen bonds : angle 3.78580 ( 1922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.597 Fit side-chains REVERT: A 681 MET cc_start: 0.9234 (tpt) cc_final: 0.8916 (tpp) REVERT: A 872 MET cc_start: 0.9434 (mtm) cc_final: 0.9081 (mtt) REVERT: B 224 MET cc_start: 0.9708 (mmm) cc_final: 0.9424 (mmm) REVERT: B 599 MET cc_start: 0.9055 (mmm) cc_final: 0.8796 (mmm) REVERT: B 681 MET cc_start: 0.9473 (tpp) cc_final: 0.9227 (tpp) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.1062 time to fit residues: 6.3031 Evaluate side-chains 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 143 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.027327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.019773 restraints weight = 783322.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.020968 restraints weight = 162128.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.021848 restraints weight = 81597.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.022446 restraints weight = 52469.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.022882 restraints weight = 38411.482| |-----------------------------------------------------------------------------| r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13724 Z= 0.088 Angle : 0.509 10.213 18672 Z= 0.251 Chirality : 0.040 0.166 2090 Planarity : 0.004 0.049 2520 Dihedral : 3.261 17.371 1994 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 1.10 % Allowed : 6.96 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1812 helix: 2.69 (0.19), residues: 766 sheet: 0.95 (0.35), residues: 226 loop : -0.21 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.008 0.001 TYR B 641 PHE 0.011 0.001 PHE A 585 TRP 0.011 0.001 TRP A 54 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00198 (13724) covalent geometry : angle 0.50902 (18672) hydrogen bonds : bond 0.02785 ( 681) hydrogen bonds : angle 3.73852 ( 1922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.600 Fit side-chains REVERT: A 681 MET cc_start: 0.9212 (tpt) cc_final: 0.8886 (tpp) REVERT: A 872 MET cc_start: 0.9423 (mtm) cc_final: 0.9064 (mtt) REVERT: B 224 MET cc_start: 0.9716 (mmm) cc_final: 0.9477 (mmm) REVERT: B 599 MET cc_start: 0.9066 (mmm) cc_final: 0.8799 (mmm) REVERT: B 681 MET cc_start: 0.9451 (tpp) cc_final: 0.9204 (tpp) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.1075 time to fit residues: 6.8292 Evaluate side-chains 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 631 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 0.0970 chunk 152 optimal weight: 2.9990 chunk 71 optimal weight: 0.0470 chunk 56 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.027511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.019911 restraints weight = 846485.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.021112 restraints weight = 166483.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.022006 restraints weight = 83469.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.022627 restraints weight = 53339.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.023059 restraints weight = 38889.126| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13724 Z= 0.082 Angle : 0.507 10.111 18672 Z= 0.248 Chirality : 0.040 0.164 2090 Planarity : 0.004 0.052 2520 Dihedral : 3.211 17.321 1994 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 1.03 % Allowed : 7.11 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.20), residues: 1812 helix: 2.72 (0.19), residues: 766 sheet: 1.00 (0.35), residues: 226 loop : -0.18 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.009 0.001 TYR A 11 PHE 0.012 0.001 PHE A 585 TRP 0.010 0.001 TRP A 54 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00183 (13724) covalent geometry : angle 0.50743 (18672) hydrogen bonds : bond 0.02716 ( 681) hydrogen bonds : angle 3.71732 ( 1922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.47 seconds wall clock time: 38 minutes 21.14 seconds (2301.14 seconds total)