Starting phenix.real_space_refine on Thu Jul 31 13:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjp_41307/07_2025/8tjp_41307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjp_41307/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjp_41307/07_2025/8tjp_41307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjp_41307/07_2025/8tjp_41307.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjp_41307/07_2025/8tjp_41307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjp_41307/07_2025/8tjp_41307.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 15.38, per 1000 atoms: 1.14 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: 3.64 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 1.90 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: 5.19 Time building geometry restraints manager: 4.28 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: 0.08 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: 10.130 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 45.020 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP B 602 HIS 0.003 0.001 HIS B 338 PHE 0.011 0.001 PHE B 103 TYR 0.010 0.001 TYR B 823 ARG 0.005 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.17117 ( 681) hydrogen bonds : angle 5.87775 ( 1922) covalent geometry : bond 0.00294 (13724) covalent geometry : angle 0.60447 (18672) *********************** 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 : 1.442 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2402 time to fit residues: 18.0606 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 : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.2750 r_free = 0.2750 target = 0.027987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.020074 restraints weight = 873456.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.021306 restraints weight = 168953.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.022212 restraints weight = 84490.428| |-----------------------------------------------------------------------------| r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1399 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= 0.147 Angle : 0.588 8.516 18672 Z= 0.302 Chirality : 0.043 0.147 2090 Planarity : 0.005 0.048 2520 Dihedral : 3.828 19.645 1994 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1812 helix: 2.40 (0.19), residues: 742 sheet: 0.57 (0.34), residues: 228 loop : -0.55 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 801 HIS 0.004 0.001 HIS A 79 PHE 0.013 0.001 PHE A 242 TYR 0.011 0.001 TYR B 800 ARG 0.009 0.001 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 681) hydrogen bonds : angle 4.40684 ( 1922) covalent geometry : bond 0.00323 (13724) covalent geometry : angle 0.58792 (18672) *********************** 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 45 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8785 (ptm) cc_final: 0.8330 (ptm) REVERT: A 596 MET cc_start: 0.9576 (mtp) cc_final: 0.9369 (mtp) REVERT: A 681 MET cc_start: 0.9201 (tpt) cc_final: 0.8825 (tpt) REVERT: A 690 MET cc_start: 0.8485 (mtt) cc_final: 0.8049 (mpp) REVERT: B 224 MET cc_start: 0.9709 (mmm) cc_final: 0.9398 (mmm) REVERT: B 681 MET cc_start: 0.9560 (tpp) cc_final: 0.9350 (tpp) outliers start: 6 outliers final: 0 residues processed: 43 average time/residue: 0.2758 time to fit residues: 20.2102 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 : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 chunk 171 optimal weight: 0.0370 chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN B 51 GLN B 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.027528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.019769 restraints weight = 838562.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.020955 restraints weight = 167104.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.021845 restraints weight = 84637.921| |-----------------------------------------------------------------------------| r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13724 Z= 0.133 Angle : 0.550 7.220 18672 Z= 0.280 Chirality : 0.041 0.150 2090 Planarity : 0.004 0.047 2520 Dihedral : 3.690 17.525 1994 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.88 % Allowed : 7.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1812 helix: 2.53 (0.19), residues: 748 sheet: 0.72 (0.34), residues: 228 loop : -0.33 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 801 HIS 0.003 0.001 HIS B 517 PHE 0.010 0.001 PHE A 585 TYR 0.008 0.001 TYR A 802 ARG 0.005 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 681) hydrogen bonds : angle 4.13133 ( 1922) covalent geometry : bond 0.00292 (13724) covalent geometry : angle 0.55013 (18672) *********************** 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 39 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 MET cc_start: 0.9535 (mtp) cc_final: 0.9245 (mtp) REVERT: A 681 MET cc_start: 0.9147 (tpt) cc_final: 0.8779 (tpt) REVERT: B 224 MET cc_start: 0.9705 (mmm) cc_final: 0.9485 (mmm) REVERT: B 680 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9448 (mp) REVERT: B 681 MET cc_start: 0.9568 (tpp) cc_final: 0.9348 (tpp) outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 0.3236 time to fit residues: 26.1511 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 : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 680 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.026390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.018899 restraints weight = 838425.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.020048 restraints weight = 168698.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.020896 restraints weight = 84874.316| |-----------------------------------------------------------------------------| r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13724 Z= 0.188 Angle : 0.588 8.755 18672 Z= 0.298 Chirality : 0.041 0.208 2090 Planarity : 0.005 0.048 2520 Dihedral : 3.831 18.474 1994 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.95 % Allowed : 7.26 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1812 helix: 2.33 (0.19), residues: 768 sheet: 0.57 (0.33), residues: 234 loop : -0.39 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 801 HIS 0.005 0.001 HIS A 660 PHE 0.009 0.001 PHE A 585 TYR 0.010 0.002 TYR A 802 ARG 0.005 0.001 ARG B 705 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 681) hydrogen bonds : angle 4.21148 ( 1922) covalent geometry : bond 0.00403 (13724) covalent geometry : angle 0.58779 (18672) *********************** 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 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 MET cc_start: 0.9545 (mtp) cc_final: 0.9265 (ptm) REVERT: A 681 MET cc_start: 0.9176 (tpt) cc_final: 0.8812 (tpt) REVERT: A 872 MET cc_start: 0.9254 (mtm) cc_final: 0.8924 (ptp) REVERT: B 224 MET cc_start: 0.9697 (mmm) cc_final: 0.9466 (mmm) REVERT: B 681 MET cc_start: 0.9588 (tpp) cc_final: 0.9295 (tpt) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.2412 time to fit residues: 16.2083 Evaluate side-chains 33 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2722 r_free = 0.2722 target = 0.027287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.019615 restraints weight = 860901.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.020805 restraints weight = 166106.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.021696 restraints weight = 83038.036| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13724 Z= 0.093 Angle : 0.514 8.406 18672 Z= 0.257 Chirality : 0.041 0.143 2090 Planarity : 0.004 0.050 2520 Dihedral : 3.529 18.800 1994 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.95 % Allowed : 7.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1812 helix: 2.62 (0.19), residues: 752 sheet: 0.75 (0.35), residues: 230 loop : -0.21 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.002 0.001 HIS B 338 PHE 0.012 0.001 PHE A 585 TYR 0.007 0.001 TYR B 641 ARG 0.004 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 681) hydrogen bonds : angle 3.90300 ( 1922) covalent geometry : bond 0.00207 (13724) covalent geometry : angle 0.51389 (18672) *********************** 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 36 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 4.058 Fit side-chains revert: symmetry clash REVERT: A 681 MET cc_start: 0.9212 (tpt) cc_final: 0.8813 (tpt) REVERT: B 224 MET cc_start: 0.9686 (mmm) cc_final: 0.9476 (mmm) REVERT: B 599 MET cc_start: 0.9233 (mmm) cc_final: 0.8955 (mmm) REVERT: B 681 MET cc_start: 0.9558 (tpp) cc_final: 0.9267 (tpt) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.4067 time to fit residues: 25.0481 Evaluate side-chains 33 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.019526 restraints weight = 820982.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.020715 restraints weight = 165161.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021592 restraints weight = 83159.443| |-----------------------------------------------------------------------------| r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2879 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= 0.103 Angle : 0.517 8.556 18672 Z= 0.258 Chirality : 0.040 0.171 2090 Planarity : 0.004 0.051 2520 Dihedral : 3.470 20.196 1994 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.95 % Allowed : 7.26 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1812 helix: 2.64 (0.19), residues: 764 sheet: 0.68 (0.34), residues: 236 loop : -0.25 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.003 0.001 HIS A 660 PHE 0.011 0.001 PHE A 585 TYR 0.006 0.001 TYR B 11 ARG 0.004 0.000 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 681) hydrogen bonds : angle 3.85977 ( 1922) covalent geometry : bond 0.00230 (13724) covalent geometry : angle 0.51655 (18672) *********************** 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 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 2.243 Fit side-chains REVERT: A 681 MET cc_start: 0.9212 (tpt) cc_final: 0.8889 (tpp) REVERT: B 224 MET cc_start: 0.9697 (mmm) cc_final: 0.9475 (mmm) REVERT: B 681 MET cc_start: 0.9570 (tpp) cc_final: 0.9266 (tpt) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.2686 time to fit residues: 18.1162 Evaluate side-chains 33 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 chunk 150 optimal weight: 0.0470 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.027641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.020090 restraints weight = 763426.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.021295 restraints weight = 158827.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.022178 restraints weight = 80383.543| |-----------------------------------------------------------------------------| r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13724 Z= 0.083 Angle : 0.498 11.384 18672 Z= 0.247 Chirality : 0.040 0.185 2090 Planarity : 0.004 0.048 2520 Dihedral : 3.327 19.229 1994 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.95 % Allowed : 7.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.20), residues: 1812 helix: 2.65 (0.19), residues: 768 sheet: 0.96 (0.35), residues: 226 loop : -0.22 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.002 0.001 HIS B 338 PHE 0.011 0.001 PHE A 585 TYR 0.008 0.001 TYR B 641 ARG 0.003 0.000 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 681) hydrogen bonds : angle 3.74522 ( 1922) covalent geometry : bond 0.00185 (13724) covalent geometry : angle 0.49786 (18672) *********************** 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: 3 poor density : 32 time to evaluate : 2.241 Fit side-chains REVERT: A 681 MET cc_start: 0.9222 (tpt) cc_final: 0.8907 (tpp) REVERT: B 224 MET cc_start: 0.9713 (mmm) cc_final: 0.9490 (mmm) REVERT: B 599 MET cc_start: 0.9024 (mmm) cc_final: 0.8754 (mmm) REVERT: B 681 MET cc_start: 0.9537 (tpp) cc_final: 0.9231 (tpt) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.4416 time to fit residues: 25.4703 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 : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 606 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 175 optimal weight: 0.0980 chunk 168 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 172 optimal weight: 7.9990 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 405 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.027627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.019966 restraints weight = 915813.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.021193 restraints weight = 171110.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.022093 restraints weight = 84659.516| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.3137 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= 0.089 Angle : 0.505 10.594 18672 Z= 0.251 Chirality : 0.040 0.157 2090 Planarity : 0.004 0.050 2520 Dihedral : 3.300 19.253 1994 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.03 % Allowed : 7.18 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.20), residues: 1812 helix: 2.67 (0.19), residues: 768 sheet: 0.98 (0.35), residues: 226 loop : -0.20 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.002 0.001 HIS A 80 PHE 0.013 0.001 PHE A 868 TYR 0.007 0.001 TYR B 11 ARG 0.003 0.000 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.02828 ( 681) hydrogen bonds : angle 3.72142 ( 1922) covalent geometry : bond 0.00199 (13724) covalent geometry : angle 0.50480 (18672) *********************** 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: 4 poor density : 32 time to evaluate : 2.295 Fit side-chains REVERT: A 681 MET cc_start: 0.9228 (tpt) cc_final: 0.8914 (tpp) REVERT: B 224 MET cc_start: 0.9720 (mmm) cc_final: 0.9505 (mmm) REVERT: B 596 MET cc_start: 0.9369 (tpp) cc_final: 0.9019 (tmm) REVERT: B 599 MET cc_start: 0.9088 (mmm) cc_final: 0.8798 (mmm) REVERT: B 631 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (ttt) REVERT: B 681 MET cc_start: 0.9526 (tpp) cc_final: 0.9272 (tpp) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.3974 time to fit residues: 24.3767 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 : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 631 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2737 r_free = 0.2737 target = 0.027532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.020076 restraints weight = 804863.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.021280 restraints weight = 162496.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.022158 restraints weight = 81630.143| |-----------------------------------------------------------------------------| r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13724 Z= 0.091 Angle : 0.509 11.591 18672 Z= 0.251 Chirality : 0.040 0.264 2090 Planarity : 0.004 0.050 2520 Dihedral : 3.259 18.803 1994 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 0.95 % Allowed : 7.04 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1812 helix: 2.69 (0.19), residues: 766 sheet: 0.89 (0.34), residues: 232 loop : -0.20 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.002 0.001 HIS A 80 PHE 0.010 0.001 PHE A 585 TYR 0.006 0.001 TYR A 11 ARG 0.003 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 681) hydrogen bonds : angle 3.73848 ( 1922) covalent geometry : bond 0.00205 (13724) covalent geometry : angle 0.50925 (18672) *********************** 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: 3 poor density : 33 time to evaluate : 1.601 Fit side-chains REVERT: A 681 MET cc_start: 0.9259 (tpt) cc_final: 0.8951 (tpp) REVERT: A 872 MET cc_start: 0.9435 (mtm) cc_final: 0.9067 (mtt) REVERT: B 224 MET cc_start: 0.9730 (mmm) cc_final: 0.9497 (mmm) REVERT: B 596 MET cc_start: 0.9367 (tpp) cc_final: 0.8990 (tmm) REVERT: B 599 MET cc_start: 0.9047 (mmm) cc_final: 0.8724 (mmm) REVERT: B 631 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8765 (ttt) REVERT: B 681 MET cc_start: 0.9544 (tpp) cc_final: 0.9289 (tpp) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.2487 time to fit residues: 15.6414 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 : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 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 18 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 130 optimal weight: 0.0670 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.2749 r_free = 0.2749 target = 0.027820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.020236 restraints weight = 855595.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021468 restraints weight = 164463.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.022360 restraints weight = 81884.550| |-----------------------------------------------------------------------------| r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13724 Z= 0.081 Angle : 0.502 10.912 18672 Z= 0.246 Chirality : 0.040 0.254 2090 Planarity : 0.004 0.051 2520 Dihedral : 3.198 19.593 1994 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 0.88 % Allowed : 7.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.20), residues: 1812 helix: 2.69 (0.19), residues: 768 sheet: 0.97 (0.35), residues: 226 loop : -0.13 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.002 0.000 HIS B 338 PHE 0.011 0.001 PHE A 585 TYR 0.012 0.001 TYR B 641 ARG 0.003 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.02703 ( 681) hydrogen bonds : angle 3.70440 ( 1922) covalent geometry : bond 0.00182 (13724) covalent geometry : angle 0.50156 (18672) ********************** 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 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 1.644 Fit side-chains REVERT: A 681 MET cc_start: 0.9268 (tpt) cc_final: 0.8940 (tpp) REVERT: A 872 MET cc_start: 0.9413 (mtm) cc_final: 0.9054 (mtt) REVERT: B 596 MET cc_start: 0.9392 (tpp) cc_final: 0.9006 (tmm) REVERT: B 599 MET cc_start: 0.9033 (mmm) cc_final: 0.8723 (mmm) REVERT: B 631 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8754 (ttt) REVERT: B 681 MET cc_start: 0.9551 (tpp) cc_final: 0.9290 (tpp) outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.2482 time to fit residues: 16.3270 Evaluate side-chains 35 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET 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 85 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 = 0.2733 r_free = 0.2733 target = 0.027391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.019836 restraints weight = 843367.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.021044 restraints weight = 167687.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.021918 restraints weight = 84115.014| |-----------------------------------------------------------------------------| r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13724 Z= 0.105 Angle : 0.519 11.327 18672 Z= 0.254 Chirality : 0.040 0.243 2090 Planarity : 0.004 0.049 2520 Dihedral : 3.236 18.403 1994 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1812 helix: 2.71 (0.19), residues: 772 sheet: 0.84 (0.34), residues: 232 loop : -0.13 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.001 PHE A 585 TYR 0.014 0.001 TYR B 641 ARG 0.003 0.000 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 681) hydrogen bonds : angle 3.75920 ( 1922) covalent geometry : bond 0.00234 (13724) covalent geometry : angle 0.51899 (18672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5174.85 seconds wall clock time: 101 minutes 47.52 seconds (6107.52 seconds total)