Starting phenix.real_space_refine on Wed Aug 5 09:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9saq_54694/08_2026/9saq_54694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9saq_54694/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9saq_54694/08_2026/9saq_54694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9saq_54694/08_2026/9saq_54694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9saq_54694/08_2026/9saq_54694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9saq_54694/08_2026/9saq_54694.map" } 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-2.2rc3-6140/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: 1.97, per 1000 atoms: 0.21 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: 0.67 Conformation dependent library (CDL) restraints added in 203.1 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: 1.05 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: 1.59 Time building geometry restraints manager: 0.88 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: 12396 1.94 - 3.88: 642 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: 1191 0.060 - 0.119: 216 0.119 - 0.179: 78 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: 0.280 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.980 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- 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= 0.429 Angle : 0.893 9.705 13151 Z= 0.624 Chirality : 0.057 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 0.00597 / 0.43 ( 9580) covalent geometry : angle 0.89260 / 0.62 (13145) hydrogen bonds : bond 0.16412 / 17.33 ( 437) hydrogen bonds : angle 6.61669 / 6.91 ( 1307) metal coordination : bond 0.00323 / 0.22 ( 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 : 0.279 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: 0.0934 time to fit residues: 18.7379 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 : 0.240 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.127419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.097131 restraints weight = 10878.059| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.35 r_work: 0.2798 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0826 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= 0.162 Angle : 0.538 9.528 13151 Z= 0.296 Chirality : 0.042 0.145 1499 Planarity : 0.004 0.032 1564 Dihedral : 11.911 84.928 1673 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.49 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: 0.01 (0.25), residues: 1072 helix: 0.86 (0.25), residues: 487 sheet: 0.21 (0.47), residues: 116 loop : -0.90 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.020 0.002 TYR A 515 PHE 0.017 0.002 PHE A 881 TRP 0.011 0.002 TRP A 290 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9580) covalent geometry : angle 0.53760 / 0.30 (13145) hydrogen bonds : bond 0.05922 / 6.29 ( 437) hydrogen bonds : angle 4.78352 / 5.35 ( 1307) metal coordination : bond 0.00334 / 0.22 ( 8) metal coordination : angle 1.54375 / 2.90 ( 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 122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.330 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 121 average time/residue: 0.0829 time to fit residues: 14.2817 Evaluate side-chains 117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 0.9990 chunk 91 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099421 restraints weight = 10772.795| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.34 r_work: 0.2859 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9588 Z= 0.104 Angle : 0.444 8.568 13151 Z= 0.247 Chirality : 0.039 0.142 1499 Planarity : 0.003 0.030 1564 Dihedral : 11.394 81.351 1656 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 9.02 % Favored : 89.51 % 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: 0.33 (0.26), residues: 1072 helix: 1.20 (0.25), residues: 489 sheet: 0.38 (0.47), residues: 118 loop : -0.86 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.012 0.001 TYR A 515 PHE 0.019 0.001 PHE A 340 TRP 0.006 0.001 TRP A 598 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9580) covalent geometry : angle 0.44390 / 0.25 (13145) hydrogen bonds : bond 0.04331 / 4.68 ( 437) hydrogen bonds : angle 4.30629 / 4.86 ( 1307) metal coordination : bond 0.00305 / 0.19 ( 8) metal coordination : angle 1.02046 / 2.03 ( 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 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.257 Fit side-chains REVERT: A 39 ASN cc_start: 0.7861 (m110) cc_final: 0.7643 (m110) REVERT: A 334 PHE cc_start: 0.7734 (m-80) cc_final: 0.7387 (m-80) REVERT: A 883 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8287 (tp) REVERT: C 52 MET cc_start: 0.7481 (ttp) cc_final: 0.7219 (ttt) outliers start: 14 outliers final: 12 residues processed: 121 average time/residue: 0.0805 time to fit residues: 13.8770 Evaluate side-chains 114 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.095014 restraints weight = 10939.171| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.26 r_work: 0.2742 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9588 Z= 0.238 Angle : 0.591 10.960 13151 Z= 0.320 Chirality : 0.046 0.159 1499 Planarity : 0.004 0.040 1564 Dihedral : 11.436 81.458 1650 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 10.07 % Favored : 87.41 % 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: 0.00 (0.25), residues: 1072 helix: 0.94 (0.24), residues: 485 sheet: 0.30 (0.47), residues: 116 loop : -1.05 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.021 0.002 TYR A 515 PHE 0.021 0.002 PHE A 348 TRP 0.014 0.002 TRP A 290 HIS 0.007 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 ( 9580) covalent geometry : angle 0.58847 / 0.32 (13145) hydrogen bonds : bond 0.06201 / 6.65 ( 437) hydrogen bonds : angle 4.53308 / 5.19 ( 1307) metal coordination : bond 0.00711 / 0.43 ( 8) metal coordination : angle 2.44302 / 4.40 ( 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 129 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.335 Fit side-chains REVERT: A 244 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8869 (mp) outliers start: 24 outliers final: 18 residues processed: 123 average time/residue: 0.0777 time to fit residues: 13.7826 Evaluate side-chains 122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 341 VAL 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 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: 0.5980 chunk 14 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.127037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.096616 restraints weight = 10796.661| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.34 r_work: 0.2801 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9588 Z= 0.133 Angle : 0.479 10.469 13151 Z= 0.264 Chirality : 0.041 0.158 1499 Planarity : 0.003 0.032 1564 Dihedral : 11.314 81.440 1650 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.99 % Allowed : 11.12 % Favored : 86.88 % 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: 0.18 (0.25), residues: 1072 helix: 1.08 (0.25), residues: 489 sheet: 0.32 (0.47), residues: 118 loop : -0.95 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.015 0.001 TYR A 515 PHE 0.017 0.001 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 0.00305 / 0.13 ( 9580) covalent geometry : angle 0.47794 / 0.26 (13145) hydrogen bonds : bond 0.04938 / 5.32 ( 437) hydrogen bonds : angle 4.32827 / 4.95 ( 1307) metal coordination : bond 0.00405 / 0.23 ( 8) metal coordination : angle 1.41486 / 2.70 ( 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 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.324 Fit side-chains outliers start: 19 outliers final: 17 residues processed: 121 average time/residue: 0.0773 time to fit residues: 13.5415 Evaluate side-chains 117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 235 ASP 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 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: 10.0000 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.125364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.095803 restraints weight = 10856.724| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.21 r_work: 0.2761 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9588 Z= 0.185 Angle : 0.540 11.092 13151 Z= 0.294 Chirality : 0.044 0.166 1499 Planarity : 0.004 0.033 1564 Dihedral : 11.341 83.306 1648 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.41 % Allowed : 11.65 % Favored : 85.94 % 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: 1.01 (0.24), residues: 488 sheet: 0.33 (0.48), residues: 116 loop : -1.00 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.018 0.002 TYR A 515 PHE 0.017 0.002 PHE A 741 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 0.53849 / 0.29 (13145) hydrogen bonds : bond 0.05672 / 6.10 ( 437) hydrogen bonds : angle 4.41346 / 5.07 ( 1307) metal coordination : bond 0.00512 / 0.32 ( 8) metal coordination : angle 2.06279 / 3.78 ( 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 129 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.248 Fit side-chains REVERT: A 39 ASN cc_start: 0.8169 (m110) cc_final: 0.7904 (m110) REVERT: A 370 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7879 (mt-10) REVERT: A 798 LYS cc_start: 0.7941 (mppt) cc_final: 0.7737 (mptt) REVERT: B 155 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8047 (tt0) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 0.0787 time to fit residues: 14.2937 Evaluate side-chains 124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 235 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 33 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 overall best weight: 2.5396 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.127360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096970 restraints weight = 10845.423| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.33 r_work: 0.2810 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9588 Z= 0.120 Angle : 0.469 10.622 13151 Z= 0.258 Chirality : 0.040 0.160 1499 Planarity : 0.003 0.033 1564 Dihedral : 11.226 82.013 1648 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.20 % Allowed : 11.75 % Favored : 86.04 % 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: 0.24 (0.25), residues: 1072 helix: 1.13 (0.25), residues: 489 sheet: 0.29 (0.47), residues: 118 loop : -0.90 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.013 0.001 TYR A 149 PHE 0.016 0.001 PHE A 881 TRP 0.010 0.001 TRP A 290 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9580) covalent geometry : angle 0.46773 / 0.26 (13145) hydrogen bonds : bond 0.04729 / 5.11 ( 437) hydrogen bonds : angle 4.25591 / 4.89 ( 1307) metal coordination : bond 0.00400 / 0.28 ( 8) metal coordination : angle 1.36317 / 2.63 ( 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 130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.332 Fit side-chains REVERT: A 39 ASN cc_start: 0.7868 (m110) cc_final: 0.7622 (m110) REVERT: A 370 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7774 (mt-10) REVERT: A 798 LYS cc_start: 0.7855 (mppt) cc_final: 0.7645 (mptt) outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 0.0802 time to fit residues: 14.9195 Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain A residue 235 ASP 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 687 THR Chi-restraints excluded: chain A residue 726 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.128139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097323 restraints weight = 10703.319| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.30 r_work: 0.2819 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9588 Z= 0.112 Angle : 0.453 9.928 13151 Z= 0.250 Chirality : 0.040 0.165 1499 Planarity : 0.003 0.033 1564 Dihedral : 11.121 79.967 1647 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.10 % Allowed : 12.28 % 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: 0.37 (0.26), residues: 1072 helix: 1.23 (0.25), residues: 489 sheet: 0.36 (0.47), residues: 118 loop : -0.81 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.012 0.001 TYR A 515 PHE 0.015 0.001 PHE A 881 TRP 0.008 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9580) covalent geometry : angle 0.45216 / 0.25 (13145) hydrogen bonds : bond 0.04411 / 4.78 ( 437) hydrogen bonds : angle 4.15985 / 4.79 ( 1307) metal coordination : bond 0.00374 / 0.26 ( 8) metal coordination : angle 1.18252 / 2.30 ( 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 129 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.315 Fit side-chains REVERT: A 39 ASN cc_start: 0.7907 (m110) cc_final: 0.7697 (m110) REVERT: A 334 PHE cc_start: 0.7681 (m-80) cc_final: 0.7235 (m-80) REVERT: A 370 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7740 (mt-10) REVERT: B 155 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7846 (tt0) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.0716 time to fit residues: 12.8876 Evaluate side-chains 121 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain A residue 235 ASP 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 687 THR Chi-restraints excluded: chain A residue 726 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 0.5980 chunk 65 optimal weight: 0.0870 chunk 51 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 875 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101131 restraints weight = 10740.201| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.37 r_work: 0.2885 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9588 Z= 0.087 Angle : 0.414 9.040 13151 Z= 0.228 Chirality : 0.038 0.164 1499 Planarity : 0.003 0.031 1564 Dihedral : 11.002 73.853 1646 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 13.64 % Favored : 85.41 % 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: 0.55 (0.26), residues: 1072 helix: 1.34 (0.25), residues: 493 sheet: 0.44 (0.47), residues: 118 loop : -0.69 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.011 0.001 TYR A 831 PHE 0.014 0.001 PHE A 881 TRP 0.008 0.001 TRP A 598 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.09 ( 9580) covalent geometry : angle 0.41310 / 0.23 (13145) hydrogen bonds : bond 0.03529 / 3.87 ( 437) hydrogen bonds : angle 4.00227 / 4.61 ( 1307) metal coordination : bond 0.00380 / 0.31 ( 8) metal coordination : angle 1.15959 / 2.28 ( 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 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.221 Fit side-chains REVERT: A 74 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7684 (mtt90) REVERT: A 334 PHE cc_start: 0.7675 (m-80) cc_final: 0.7359 (m-80) REVERT: A 370 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7762 (mt-10) REVERT: A 610 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 155 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: B 176 ASN cc_start: 0.8313 (t0) cc_final: 0.8006 (t0) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.0794 time to fit residues: 13.6851 Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 928 HIS 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: 9.9990 chunk 70 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.124752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094069 restraints weight = 10810.557| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.26 r_work: 0.2756 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1520 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= 0.231 Angle : 0.594 10.770 13151 Z= 0.321 Chirality : 0.047 0.204 1499 Planarity : 0.005 0.040 1564 Dihedral : 11.123 80.278 1642 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.05 % Allowed : 14.27 % Favored : 84.68 % 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: 0.18 (0.25), residues: 1072 helix: 1.02 (0.24), residues: 488 sheet: 0.43 (0.48), residues: 116 loop : -0.90 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 889 TYR 0.023 0.002 TYR A 515 PHE 0.021 0.002 PHE A 741 TRP 0.017 0.002 TRP A 290 HIS 0.008 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 ( 9580) covalent geometry : angle 0.59202 / 0.32 (13145) hydrogen bonds : bond 0.06143 / 6.60 ( 437) hydrogen bonds : angle 4.40716 / 5.10 ( 1307) metal coordination : bond 0.00743 / 0.48 ( 8) metal coordination : angle 2.56885 / 4.63 ( 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 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.343 Fit side-chains REVERT: A 370 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7806 (mt-10) REVERT: B 155 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7942 (tt0) outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 0.0710 time to fit residues: 12.0211 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 928 HIS 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: 3.9990 chunk 24 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097696 restraints weight = 10709.842| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.24 r_work: 0.2817 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9588 Z= 0.106 Angle : 0.464 10.342 13151 Z= 0.258 Chirality : 0.040 0.218 1499 Planarity : 0.003 0.033 1564 Dihedral : 10.983 79.421 1642 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.15 % Allowed : 14.48 % Favored : 84.37 % 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: 0.36 (0.26), residues: 1072 helix: 1.19 (0.25), residues: 489 sheet: 0.39 (0.47), residues: 118 loop : -0.81 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.013 0.001 TYR A 149 PHE 0.018 0.001 PHE A 881 TRP 0.010 0.001 TRP A 290 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 9580) covalent geometry : angle 0.46330 / 0.26 (13145) hydrogen bonds : bond 0.04518 / 4.91 ( 437) hydrogen bonds : angle 4.21878 / 4.86 ( 1307) metal coordination : bond 0.00355 / 0.21 ( 8) metal coordination : angle 1.34049 / 2.62 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.77 seconds wall clock time: 34 minutes 34.19 seconds (2074.19 seconds total)