Starting phenix.real_space_refine on Thu Jul 2 16:28:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9saq_54694/07_2026/9saq_54694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9saq_54694/07_2026/9saq_54694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9saq_54694/07_2026/9saq_54694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9saq_54694/07_2026/9saq_54694.map" model { file = "/net/cci-nas-00/data/ceres_data/9saq_54694/07_2026/9saq_54694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9saq_54694/07_2026/9saq_54694.cif" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 31 5.49 5 S 62 5.16 5 C 5817 2.51 5 N 1560 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9305 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 7277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7277 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 874} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3037 SG CYS A 301 66.600 40.660 43.341 1.00 9.24 S ATOM 3078 SG CYS A 306 69.450 43.103 42.501 1.00 9.09 S ATOM 3110 SG CYS A 310 65.999 43.444 40.826 1.00 7.44 S ATOM 4518 SG CYS A 487 69.464 34.147 63.097 1.00 9.76 S ATOM 5771 SG CYS A 645 72.905 35.640 62.261 1.00 12.18 S ATOM 5777 SG CYS A 646 70.697 34.177 59.449 1.00 10.87 S Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 9305 At special positions: 0 Unit cell: (90.9, 100.8, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 62 16.00 P 31 15.00 O 1833 8.00 N 1560 7.00 C 5817 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: 0.60 Conformation dependent library (CDL) restraints added in 194.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 51.5% alpha, 20.5% beta 7 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.518A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.265A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.619A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.751A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.756A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.685A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.501A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.639A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.502A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.655A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.889A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.572A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.839A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.654A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.570A pdb=" N THR A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 4.029A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.740A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 896 " --> pdb=" O HIS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.642A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.187A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 21 removed outlier: 3.545A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.958A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.663A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.797A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 74 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.197A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.584A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.584A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 555 through 559 removed outlier: 4.707A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 555 through 559 removed outlier: 4.707A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 458 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2599 1.33 - 1.45: 1887 1.45 - 1.57: 4943 1.57 - 1.69: 60 1.69 - 1.81: 91 Bond restraints: 9580 Sorted by residual: bond pdb=" C ASN A 874 " pdb=" O ASN A 874 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.24e-02 6.50e+03 2.99e+01 bond pdb=" C ASP B 99 " pdb=" O ASP B 99 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.09e-02 8.42e+03 1.73e+01 bond pdb=" C MET B 94 " pdb=" O MET B 94 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.25e-02 6.40e+03 1.65e+01 bond pdb=" N VAL A 231 " pdb=" CA VAL A 231 " ideal model delta sigma weight residual 1.456 1.489 -0.033 8.60e-03 1.35e+04 1.47e+01 bond pdb=" N ILE B 106 " pdb=" CA ILE B 106 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.06e-02 8.90e+03 1.35e+01 ... (remaining 9575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12481 1.94 - 3.88: 557 3.88 - 5.82: 84 5.82 - 7.76: 17 7.76 - 9.71: 6 Bond angle restraints: 13145 Sorted by residual: angle pdb=" N PRO A 612 " pdb=" CA PRO A 612 " pdb=" C PRO A 612 " ideal model delta sigma weight residual 111.03 120.09 -9.06 1.54e+00 4.22e-01 3.46e+01 angle pdb=" C HIS A 928 " pdb=" CA HIS A 928 " pdb=" CB HIS A 928 " ideal model delta sigma weight residual 111.41 102.30 9.11 1.65e+00 3.67e-01 3.05e+01 angle pdb=" N HIS A 613 " pdb=" CA HIS A 613 " pdb=" C HIS A 613 " ideal model delta sigma weight residual 109.24 100.92 8.32 1.51e+00 4.39e-01 3.03e+01 angle pdb=" N TYR A 877 " pdb=" CA TYR A 877 " pdb=" CB TYR A 877 " ideal model delta sigma weight residual 110.19 101.66 8.53 1.55e+00 4.16e-01 3.03e+01 angle pdb=" C VAL A 880 " pdb=" N PHE A 881 " pdb=" CA PHE A 881 " ideal model delta sigma weight residual 120.44 113.70 6.74 1.30e+00 5.92e-01 2.69e+01 ... (remaining 13140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 5002 16.74 - 33.48: 506 33.48 - 50.22: 115 50.22 - 66.96: 72 66.96 - 83.70: 14 Dihedral angle restraints: 5709 sinusoidal: 2498 harmonic: 3211 Sorted by residual: dihedral pdb=" CD ARG A 735 " pdb=" NE ARG A 735 " pdb=" CZ ARG A 735 " pdb=" NH1 ARG A 735 " ideal model delta sinusoidal sigma weight residual 0.00 -72.22 72.22 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" C HIS A 928 " pdb=" N HIS A 928 " pdb=" CA HIS A 928 " pdb=" CB HIS A 928 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" CD ARG A 173 " pdb=" NE ARG A 173 " pdb=" CZ ARG A 173 " pdb=" NH1 ARG A 173 " ideal model delta sinusoidal sigma weight residual 0.00 -31.48 31.48 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 5706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1222 0.060 - 0.119: 214 0.119 - 0.179: 49 0.179 - 0.239: 9 0.239 - 0.298: 5 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA HIS A 928 " pdb=" N HIS A 928 " pdb=" C HIS A 928 " pdb=" CB HIS A 928 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA LYS A 807 " pdb=" N LYS A 807 " pdb=" C LYS A 807 " pdb=" CB LYS A 807 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL A 234 " pdb=" N VAL A 234 " pdb=" C VAL A 234 " pdb=" CB VAL A 234 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1496 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 735 " -1.053 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG A 735 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 735 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 735 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 735 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " 0.558 9.50e-02 1.11e+02 2.50e-01 3.83e+01 pdb=" NE ARG A 173 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 873 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C PRO A 873 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO A 873 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN A 874 " 0.024 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2080 2.79 - 3.32: 8220 3.32 - 3.84: 15465 3.84 - 4.37: 19138 4.37 - 4.90: 31491 Nonbonded interactions: 76394 Sorted by model distance: nonbonded pdb=" O2' U T 17 " pdb=" OG SER A 592 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP A 851 " pdb=" OG1 THR A 853 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR A 402 " pdb=" O ASN A 404 " model vdw 2.340 3.040 nonbonded pdb=" OH TYR A 294 " pdb=" OD1 ASN A 314 " model vdw 2.359 3.040 nonbonded pdb=" OD2 ASP C 44 " pdb=" OG1 THR C 46 " model vdw 2.388 3.040 ... (remaining 76389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9588 Z= 0.427 Angle : 0.870 9.705 13151 Z= 0.606 Chirality : 0.053 0.298 1499 Planarity : 0.016 0.472 1564 Dihedral : 15.930 83.699 3635 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.67 % Allowed : 3.04 % Favored : 93.28 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1072 helix: 0.33 (0.25), residues: 486 sheet: -0.02 (0.46), residues: 116 loop : -1.10 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.021 0.002 TYR A 831 PHE 0.014 0.001 PHE A 741 TRP 0.008 0.001 TRP A 290 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.43 ( 9580) covalent geometry : angle 0.87021 / 0.61 (13145) hydrogen bonds : bond 0.16412 / 15.85 ( 437) hydrogen bonds : angle 6.61669 / 6.71 ( 1307) metal coordination : bond 0.00323 / 0.19 ( 8) metal coordination : angle 0.80986 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.233 Fit side-chains REVERT: A 244 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 658 GLU cc_start: 0.7247 (tt0) cc_final: 0.7028 (tt0) REVERT: A 735 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6689 (ttp80) outliers start: 35 outliers final: 13 residues processed: 146 average time/residue: 0.0849 time to fit residues: 17.3203 Evaluate side-chains 114 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 613 HIS B 88 GLN B 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.096948 restraints weight = 10873.708| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.33 r_work: 0.2800 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9588 Z= 0.163 Angle : 0.537 9.688 13151 Z= 0.296 Chirality : 0.042 0.155 1499 Planarity : 0.004 0.032 1564 Dihedral : 11.886 84.830 1673 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.57 % Allowed : 8.29 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1072 helix: 0.88 (0.25), residues: 486 sheet: 0.22 (0.47), residues: 116 loop : -0.91 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 173 TYR 0.021 0.002 TYR A 515 PHE 0.017 0.002 PHE A 881 TRP 0.010 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9580) covalent geometry : angle 0.53586 / 0.30 (13145) hydrogen bonds : bond 0.05852 / 5.64 ( 437) hydrogen bonds : angle 4.76848 / 5.16 ( 1307) metal coordination : bond 0.00427 / 0.22 ( 8) metal coordination : angle 1.50865 / 2.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.237 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 122 average time/residue: 0.0828 time to fit residues: 14.1685 Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098997 restraints weight = 10778.779| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.23 r_work: 0.2819 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9588 Z= 0.118 Angle : 0.464 9.407 13151 Z= 0.257 Chirality : 0.040 0.146 1499 Planarity : 0.003 0.031 1564 Dihedral : 11.454 81.861 1656 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.57 % Allowed : 9.55 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1072 helix: 1.13 (0.25), residues: 489 sheet: 0.36 (0.47), residues: 118 loop : -0.91 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.014 0.001 TYR A 515 PHE 0.019 0.001 PHE A 340 TRP 0.008 0.001 TRP A 290 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9580) covalent geometry : angle 0.46333 / 0.26 (13145) hydrogen bonds : bond 0.04732 / 4.63 ( 437) hydrogen bonds : angle 4.38307 / 4.79 ( 1307) metal coordination : bond 0.00371 / 0.19 ( 8) metal coordination : angle 1.16438 / 2.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.207 Fit side-chains REVERT: A 39 ASN cc_start: 0.7936 (m110) cc_final: 0.7684 (m110) REVERT: A 883 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8349 (tp) REVERT: C 52 MET cc_start: 0.7504 (ttp) cc_final: 0.7229 (ttt) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 0.0825 time to fit residues: 13.8576 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.095619 restraints weight = 10901.927| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.26 r_work: 0.2763 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9588 Z= 0.191 Angle : 0.551 10.968 13151 Z= 0.301 Chirality : 0.044 0.154 1499 Planarity : 0.004 0.036 1564 Dihedral : 11.421 80.928 1650 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.31 % Allowed : 9.97 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1072 helix: 0.91 (0.24), residues: 492 sheet: 0.30 (0.48), residues: 116 loop : -1.02 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 190 TYR 0.021 0.002 TYR A 515 PHE 0.018 0.002 PHE A 741 TRP 0.014 0.002 TRP A 290 HIS 0.006 0.001 HIS A 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 9580) covalent geometry : angle 0.54899 / 0.30 (13145) hydrogen bonds : bond 0.05855 / 5.73 ( 437) hydrogen bonds : angle 4.48136 / 4.94 ( 1307) metal coordination : bond 0.00506 / 0.26 ( 8) metal coordination : angle 2.17420 / 3.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.251 Fit side-chains REVERT: A 244 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8866 (mp) outliers start: 22 outliers final: 18 residues processed: 125 average time/residue: 0.0722 time to fit residues: 13.0367 Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 145 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.094976 restraints weight = 10821.786| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.30 r_work: 0.2765 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9588 Z= 0.185 Angle : 0.532 11.371 13151 Z= 0.292 Chirality : 0.043 0.159 1499 Planarity : 0.004 0.033 1564 Dihedral : 11.424 83.119 1650 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.31 % Allowed : 11.02 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1072 helix: 0.97 (0.24), residues: 486 sheet: 0.33 (0.48), residues: 116 loop : -1.03 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.017 0.002 TYR A 515 PHE 0.018 0.002 PHE A 340 TRP 0.013 0.002 TRP A 290 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 9580) covalent geometry : angle 0.53075 / 0.29 (13145) hydrogen bonds : bond 0.05649 / 5.54 ( 437) hydrogen bonds : angle 4.45948 / 4.93 ( 1307) metal coordination : bond 0.00548 / 0.28 ( 8) metal coordination : angle 1.91655 / 3.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.251 Fit side-chains REVERT: A 244 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 798 LYS cc_start: 0.7862 (mppt) cc_final: 0.7662 (mptt) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.0728 time to fit residues: 12.9383 Evaluate side-chains 122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.123470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.093441 restraints weight = 10875.123| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.30 r_work: 0.2729 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9588 Z= 0.263 Angle : 0.617 12.080 13151 Z= 0.335 Chirality : 0.047 0.173 1499 Planarity : 0.005 0.041 1564 Dihedral : 11.572 84.460 1648 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.62 % Allowed : 11.86 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1072 helix: 0.77 (0.24), residues: 486 sheet: 0.24 (0.47), residues: 116 loop : -1.16 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.022 0.002 TYR A 515 PHE 0.021 0.002 PHE A 348 TRP 0.016 0.002 TRP A 290 HIS 0.008 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.26 ( 9580) covalent geometry : angle 0.61495 / 0.34 (13145) hydrogen bonds : bond 0.06681 / 6.57 ( 437) hydrogen bonds : angle 4.63618 / 5.14 ( 1307) metal coordination : bond 0.00696 / 0.36 ( 8) metal coordination : angle 2.62670 / 4.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.247 Fit side-chains REVERT: A 244 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8892 (mp) REVERT: A 370 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7843 (mt-10) REVERT: A 623 ASP cc_start: 0.8104 (p0) cc_final: 0.7882 (p0) REVERT: A 798 LYS cc_start: 0.7918 (mppt) cc_final: 0.7697 (mptt) REVERT: B 155 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7997 (tt0) outliers start: 25 outliers final: 21 residues processed: 130 average time/residue: 0.0816 time to fit residues: 14.9867 Evaluate side-chains 130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.126569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.096060 restraints weight = 10856.342| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.34 r_work: 0.2783 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9588 Z= 0.127 Angle : 0.489 11.115 13151 Z= 0.270 Chirality : 0.041 0.162 1499 Planarity : 0.003 0.034 1564 Dihedral : 11.380 83.074 1648 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.62 % Allowed : 11.75 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1072 helix: 1.03 (0.25), residues: 487 sheet: 0.33 (0.48), residues: 116 loop : -1.03 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.014 0.001 TYR A 149 PHE 0.018 0.001 PHE A 881 TRP 0.011 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9580) covalent geometry : angle 0.48771 / 0.27 (13145) hydrogen bonds : bond 0.04991 / 4.92 ( 437) hydrogen bonds : angle 4.35321 / 4.83 ( 1307) metal coordination : bond 0.00381 / 0.21 ( 8) metal coordination : angle 1.45927 / 2.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.375 Fit side-chains REVERT: A 370 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7712 (mt-10) REVERT: A 798 LYS cc_start: 0.7851 (mppt) cc_final: 0.7642 (mptt) REVERT: B 155 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7919 (tt0) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.0721 time to fit residues: 13.0833 Evaluate side-chains 124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095363 restraints weight = 10754.887| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.24 r_work: 0.2759 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9588 Z= 0.175 Angle : 0.527 11.101 13151 Z= 0.289 Chirality : 0.043 0.173 1499 Planarity : 0.004 0.034 1564 Dihedral : 11.390 83.494 1648 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.73 % Allowed : 11.96 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1072 helix: 0.99 (0.24), residues: 486 sheet: 0.27 (0.48), residues: 116 loop : -1.03 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.017 0.002 TYR A 515 PHE 0.016 0.002 PHE A 348 TRP 0.012 0.002 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 9580) covalent geometry : angle 0.52566 / 0.29 (13145) hydrogen bonds : bond 0.05480 / 5.40 ( 437) hydrogen bonds : angle 4.39253 / 4.87 ( 1307) metal coordination : bond 0.00506 / 0.27 ( 8) metal coordination : angle 1.90541 / 3.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.231 Fit side-chains REVERT: A 370 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7774 (mt-10) REVERT: B 155 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7965 (tt0) outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.0780 time to fit residues: 13.7557 Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.095826 restraints weight = 10776.989| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.29 r_work: 0.2780 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9588 Z= 0.146 Angle : 0.501 10.943 13151 Z= 0.276 Chirality : 0.042 0.173 1499 Planarity : 0.004 0.034 1564 Dihedral : 11.366 83.232 1648 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.31 % Allowed : 12.49 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1072 helix: 1.04 (0.24), residues: 486 sheet: 0.29 (0.47), residues: 116 loop : -1.00 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.015 0.002 TYR A 38 PHE 0.017 0.001 PHE A 881 TRP 0.011 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9580) covalent geometry : angle 0.49941 / 0.28 (13145) hydrogen bonds : bond 0.05156 / 5.08 ( 437) hydrogen bonds : angle 4.34226 / 4.81 ( 1307) metal coordination : bond 0.00469 / 0.25 ( 8) metal coordination : angle 1.67549 / 3.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.228 Fit side-chains REVERT: A 370 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7719 (mt-10) REVERT: B 155 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7893 (tt0) outliers start: 22 outliers final: 21 residues processed: 122 average time/residue: 0.0797 time to fit residues: 13.8207 Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.094548 restraints weight = 10807.315| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.31 r_work: 0.2752 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9588 Z= 0.198 Angle : 0.550 11.367 13151 Z= 0.301 Chirality : 0.044 0.186 1499 Planarity : 0.004 0.034 1564 Dihedral : 11.432 83.863 1648 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.31 % Allowed : 12.59 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1072 helix: 0.94 (0.24), residues: 486 sheet: 0.28 (0.47), residues: 116 loop : -1.07 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 889 TYR 0.018 0.002 TYR A 515 PHE 0.017 0.002 PHE A 741 TRP 0.014 0.002 TRP A 290 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 9580) covalent geometry : angle 0.54852 / 0.30 (13145) hydrogen bonds : bond 0.05767 / 5.68 ( 437) hydrogen bonds : angle 4.44239 / 4.91 ( 1307) metal coordination : bond 0.00547 / 0.28 ( 8) metal coordination : angle 2.11145 / 3.88 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.243 Fit side-chains REVERT: A 370 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7743 (mt-10) REVERT: B 155 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7923 (tt0) outliers start: 22 outliers final: 21 residues processed: 123 average time/residue: 0.0832 time to fit residues: 14.6396 Evaluate side-chains 126 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.098127 restraints weight = 10722.886| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.28 r_work: 0.2823 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9588 Z= 0.103 Angle : 0.452 10.184 13151 Z= 0.250 Chirality : 0.040 0.181 1499 Planarity : 0.003 0.034 1564 Dihedral : 11.243 81.016 1648 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.36 % Allowed : 13.75 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1072 helix: 1.20 (0.25), residues: 488 sheet: 0.32 (0.47), residues: 118 loop : -0.88 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.013 0.001 TYR A 831 PHE 0.017 0.001 PHE A 881 TRP 0.009 0.001 TRP A 290 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9580) covalent geometry : angle 0.45167 / 0.25 (13145) hydrogen bonds : bond 0.04225 / 4.17 ( 437) hydrogen bonds : angle 4.19592 / 4.64 ( 1307) metal coordination : bond 0.00407 / 0.25 ( 8) metal coordination : angle 1.19958 / 2.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.20 seconds wall clock time: 34 minutes 32.91 seconds (2072.91 seconds total)