Starting phenix.real_space_refine on Wed Feb 4 06:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9saq_54694/02_2026/9saq_54694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9saq_54694/02_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_54694/02_2026/9saq_54694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9saq_54694/02_2026/9saq_54694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9saq_54694/02_2026/9saq_54694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9saq_54694/02_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.79, 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: 0.54 Conformation dependent library (CDL) restraints added in 412.7 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: 1.06 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: 1.60 Time building geometry restraints manager: 0.79 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: 0.240 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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= 0.425 Angle : 0.870 9.705 13151 Z= 0.604 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 covalent geometry : bond 0.00595 ( 9580) covalent geometry : angle 0.87021 (13145) hydrogen bonds : bond 0.16412 ( 437) hydrogen bonds : angle 6.61669 ( 1307) metal coordination : bond 0.00323 ( 8) metal coordination : angle 0.80986 ( 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 : 0.328 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: 0.0884 time to fit residues: 17.8332 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 : 0.348 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3333 r_free = 0.3333 target = 0.127140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.096811 restraints weight = 10847.416| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.34 r_work: 0.2796 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9588 Z= 0.160 Angle : 0.534 9.887 13151 Z= 0.291 Chirality : 0.042 0.147 1499 Planarity : 0.004 0.032 1564 Dihedral : 11.681 83.821 1673 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 8.50 % Favored : 89.93 % 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: 0.86 (0.25), residues: 484 sheet: 0.21 (0.47), residues: 116 loop : -0.98 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.020 0.002 TYR A 515 PHE 0.016 0.002 PHE A 348 TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9580) covalent geometry : angle 0.53362 (13145) hydrogen bonds : bond 0.05515 ( 437) hydrogen bonds : angle 4.63225 ( 1307) metal coordination : bond 0.00641 ( 8) metal coordination : angle 1.50082 ( 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 : 0.346 Fit side-chains REVERT: B 129 MET cc_start: 0.8733 (mtp) cc_final: 0.8528 (mtm) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 0.0856 time to fit residues: 14.2845 Evaluate side-chains 112 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 613 HIS A 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.127673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.097689 restraints weight = 10750.942| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.25 r_work: 0.2802 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9588 Z= 0.134 Angle : 0.488 10.690 13151 Z= 0.266 Chirality : 0.041 0.140 1499 Planarity : 0.004 0.032 1564 Dihedral : 11.306 79.967 1651 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.57 % Allowed : 9.65 % Favored : 88.77 % 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: 0.17 (0.25), residues: 1072 helix: 1.07 (0.25), residues: 489 sheet: 0.36 (0.47), residues: 116 loop : -0.96 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.016 0.001 TYR A 515 PHE 0.015 0.001 PHE A 348 TRP 0.010 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9580) covalent geometry : angle 0.48724 (13145) hydrogen bonds : bond 0.04791 ( 437) hydrogen bonds : angle 4.33804 ( 1307) metal coordination : bond 0.00454 ( 8) metal coordination : angle 1.30794 ( 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 122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.237 Fit side-chains REVERT: A 39 ASN cc_start: 0.7947 (m110) cc_final: 0.7713 (m110) REVERT: A 74 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7774 (mtt90) REVERT: C 52 MET cc_start: 0.7512 (ttp) cc_final: 0.7246 (ttt) outliers start: 15 outliers final: 13 residues processed: 119 average time/residue: 0.0748 time to fit residues: 12.7563 Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 208 ASP Chi-restraints excluded: chain A residue 226 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.096081 restraints weight = 10878.810| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.28 r_work: 0.2768 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1314 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= 0.158 Angle : 0.513 10.970 13151 Z= 0.279 Chirality : 0.042 0.153 1499 Planarity : 0.004 0.031 1564 Dihedral : 11.323 81.983 1647 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.78 % Allowed : 10.81 % 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: 0.15 (0.25), residues: 1072 helix: 1.07 (0.25), residues: 487 sheet: 0.33 (0.47), residues: 116 loop : -0.98 (0.26), residues: 469 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 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9580) covalent geometry : angle 0.51180 (13145) hydrogen bonds : bond 0.05178 ( 437) hydrogen bonds : angle 4.35047 ( 1307) metal coordination : bond 0.00466 ( 8) metal coordination : angle 1.75791 ( 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 127 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.242 Fit side-chains REVERT: A 39 ASN cc_start: 0.7980 (m110) cc_final: 0.7772 (m110) REVERT: A 370 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7874 (mt-10) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.0797 time to fit residues: 14.0569 Evaluate side-chains 120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 226 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 124 THR Chi-restraints excluded: chain B residue 132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.097003 restraints weight = 10771.316| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.37 r_work: 0.2798 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9588 Z= 0.133 Angle : 0.481 10.777 13151 Z= 0.262 Chirality : 0.041 0.153 1499 Planarity : 0.003 0.031 1564 Dihedral : 11.255 81.491 1647 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 11.86 % Favored : 85.83 % 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: 0.26 (0.26), residues: 1072 helix: 1.15 (0.25), residues: 487 sheet: 0.32 (0.47), residues: 118 loop : -0.90 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.014 0.001 TYR A 515 PHE 0.019 0.001 PHE A 340 TRP 0.010 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9580) covalent geometry : angle 0.48046 (13145) hydrogen bonds : bond 0.04715 ( 437) hydrogen bonds : angle 4.24130 ( 1307) metal coordination : bond 0.00422 ( 8) metal coordination : angle 1.45875 ( 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 130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.292 Fit side-chains REVERT: A 370 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7743 (mt-10) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 0.0824 time to fit residues: 15.0581 Evaluate side-chains 122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 208 ASP 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 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: 9.9990 chunk 39 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 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 = 0.3282 r_free = 0.3282 target = 0.123255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092609 restraints weight = 10900.482| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.35 r_work: 0.2716 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 9588 Z= 0.309 Angle : 0.654 11.651 13151 Z= 0.351 Chirality : 0.049 0.186 1499 Planarity : 0.005 0.041 1564 Dihedral : 11.662 86.067 1647 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.73 % Allowed : 11.86 % 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: -0.20 (0.25), residues: 1072 helix: 0.73 (0.24), residues: 486 sheet: 0.26 (0.47), residues: 116 loop : -1.12 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 889 TYR 0.022 0.003 TYR A 515 PHE 0.023 0.002 PHE A 348 TRP 0.018 0.002 TRP A 290 HIS 0.009 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 9580) covalent geometry : angle 0.65105 (13145) hydrogen bonds : bond 0.06869 ( 437) hydrogen bonds : angle 4.67545 ( 1307) metal coordination : bond 0.00806 ( 8) metal coordination : angle 2.80898 ( 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 141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.338 Fit side-chains REVERT: A 74 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7857 (mtt90) REVERT: A 370 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7821 (mt-10) REVERT: B 155 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7968 (tt0) outliers start: 26 outliers final: 21 residues processed: 135 average time/residue: 0.0857 time to fit residues: 16.4270 Evaluate side-chains 132 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 226 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 494 ILE Chi-restraints excluded: chain A residue 556 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 107 ILE 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: 0.0570 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.097388 restraints weight = 10839.942| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.29 r_work: 0.2811 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1495 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= 0.118 Angle : 0.471 11.108 13151 Z= 0.256 Chirality : 0.040 0.162 1499 Planarity : 0.003 0.033 1564 Dihedral : 11.279 81.846 1647 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.10 % Allowed : 12.49 % 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: 0.21 (0.25), residues: 1072 helix: 1.12 (0.25), residues: 488 sheet: 0.27 (0.47), residues: 118 loop : -0.93 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.012 0.001 TYR A 149 PHE 0.018 0.001 PHE A 340 TRP 0.009 0.001 TRP A 290 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9580) covalent geometry : angle 0.47040 (13145) hydrogen bonds : bond 0.04399 ( 437) hydrogen bonds : angle 4.23020 ( 1307) metal coordination : bond 0.00419 ( 8) metal coordination : angle 1.21757 ( 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: 20 poor density : 112 time to evaluate : 0.207 Fit side-chains REVERT: A 370 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7794 (mt-10) REVERT: B 176 ASN cc_start: 0.8369 (t0) cc_final: 0.8067 (t0) outliers start: 20 outliers final: 16 residues processed: 128 average time/residue: 0.0716 time to fit residues: 13.2105 Evaluate side-chains 124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 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 204 VAL Chi-restraints excluded: chain A residue 208 ASP 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 107 ILE Chi-restraints excluded: chain B residue 124 THR 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: 0.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 875 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.100842 restraints weight = 10710.072| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.34 r_work: 0.2874 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9588 Z= 0.089 Angle : 0.424 9.447 13151 Z= 0.231 Chirality : 0.039 0.163 1499 Planarity : 0.003 0.030 1564 Dihedral : 11.062 73.389 1646 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.57 % Allowed : 13.43 % Favored : 84.99 % 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: 0.56 (0.26), residues: 1072 helix: 1.31 (0.25), residues: 494 sheet: 0.45 (0.48), residues: 118 loop : -0.65 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.011 0.001 TYR A 831 PHE 0.016 0.001 PHE A 340 TRP 0.007 0.001 TRP A 598 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 9580) covalent geometry : angle 0.42394 (13145) hydrogen bonds : bond 0.03505 ( 437) hydrogen bonds : angle 4.01765 ( 1307) metal coordination : bond 0.00323 ( 8) metal coordination : angle 1.01553 ( 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 131 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.206 Fit side-chains REVERT: A 370 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7848 (mt-10) REVERT: A 610 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: B 176 ASN cc_start: 0.8289 (t0) cc_final: 0.7966 (t0) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.0838 time to fit residues: 15.0360 Evaluate side-chains 119 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 284 ASP 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 B residue 107 ILE Chi-restraints excluded: chain B residue 132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 661 GLN A 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.096262 restraints weight = 10773.008| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.24 r_work: 0.2761 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1594 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= 0.175 Angle : 0.524 10.536 13151 Z= 0.284 Chirality : 0.043 0.172 1499 Planarity : 0.004 0.031 1564 Dihedral : 11.111 76.944 1642 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.68 % Allowed : 13.75 % Favored : 84.58 % 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: 0.28 (0.26), residues: 1072 helix: 1.13 (0.25), residues: 489 sheet: 0.41 (0.48), residues: 118 loop : -0.86 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 889 TYR 0.017 0.002 TYR A 515 PHE 0.018 0.002 PHE A 340 TRP 0.013 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9580) covalent geometry : angle 0.52208 (13145) hydrogen bonds : bond 0.05236 ( 437) hydrogen bonds : angle 4.28537 ( 1307) metal coordination : bond 0.00508 ( 8) metal coordination : angle 1.88190 ( 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: 16 poor density : 107 time to evaluate : 0.364 Fit side-chains REVERT: A 370 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7806 (mt-10) REVERT: B 155 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7896 (tt0) outliers start: 16 outliers final: 12 residues processed: 121 average time/residue: 0.0818 time to fit residues: 14.0831 Evaluate side-chains 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 284 ASP 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 B residue 107 ILE 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: 4.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.095550 restraints weight = 10807.743| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.33 r_work: 0.2782 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9588 Z= 0.170 Angle : 0.521 11.038 13151 Z= 0.283 Chirality : 0.042 0.178 1499 Planarity : 0.004 0.032 1564 Dihedral : 11.143 83.656 1642 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.78 % Allowed : 13.64 % Favored : 84.58 % 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: 0.19 (0.25), residues: 1072 helix: 1.05 (0.24), residues: 489 sheet: 0.36 (0.48), residues: 118 loop : -0.91 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.016 0.002 TYR A 515 PHE 0.018 0.002 PHE A 340 TRP 0.012 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9580) covalent geometry : angle 0.51957 (13145) hydrogen bonds : bond 0.05211 ( 437) hydrogen bonds : angle 4.31475 ( 1307) metal coordination : bond 0.00500 ( 8) metal coordination : angle 1.88766 ( 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 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.243 Fit side-chains REVERT: A 370 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7831 (mt-10) REVERT: A 626 MET cc_start: 0.8238 (ttt) cc_final: 0.8002 (ttt) REVERT: B 155 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7923 (tt0) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.0810 time to fit residues: 13.9472 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 : 0.338 ------------------------------------------------------------------------------- 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 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 928 HIS Chi-restraints excluded: chain B residue 107 ILE 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: 0.0770 chunk 24 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.131017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.101007 restraints weight = 10728.366| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.26 r_work: 0.2870 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9588 Z= 0.089 Angle : 0.429 9.947 13151 Z= 0.233 Chirality : 0.039 0.171 1499 Planarity : 0.003 0.030 1564 Dihedral : 10.926 74.978 1642 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.68 % Allowed : 13.64 % 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: 0.61 (0.26), residues: 1072 helix: 1.41 (0.25), residues: 487 sheet: 0.51 (0.48), residues: 118 loop : -0.67 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.011 0.001 TYR A 38 PHE 0.017 0.001 PHE A 340 TRP 0.008 0.001 TRP A 598 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 9580) covalent geometry : angle 0.42823 (13145) hydrogen bonds : bond 0.03555 ( 437) hydrogen bonds : angle 4.02866 ( 1307) metal coordination : bond 0.00363 ( 8) metal coordination : angle 1.04601 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2043.35 seconds wall clock time: 35 minutes 35.16 seconds (2135.16 seconds total)