Starting phenix.real_space_refine on Wed Feb 4 03:14:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sao_54692/02_2026/9sao_54692.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sao_54692/02_2026/9sao_54692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sao_54692/02_2026/9sao_54692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sao_54692/02_2026/9sao_54692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sao_54692/02_2026/9sao_54692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sao_54692/02_2026/9sao_54692.map" } resolution = 2.9 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 28 5.49 5 S 58 5.16 5 C 5450 2.51 5 N 1453 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 8697 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {'F86': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "T" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 6744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6744 Classifications: {'peptide': 836} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 807} Chain breaks: 3 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} 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 2444 SG CYS A 301 66.943 41.130 38.991 1.00 47.67 S ATOM 2485 SG CYS A 306 69.601 43.687 37.988 1.00 38.83 S ATOM 2517 SG CYS A 310 66.061 43.875 36.536 1.00 34.29 S ATOM 3925 SG CYS A 487 70.183 35.078 58.533 1.00 42.63 S ATOM 5178 SG CYS A 645 73.643 36.480 57.602 1.00 50.44 S ATOM 5184 SG CYS A 646 71.394 34.826 54.899 1.00 43.00 S Time building chain proxies: 2.36, per 1000 atoms: 0.27 Number of scatterers: 8697 At special positions: 0 Unit cell: (90.9, 90.9, 112.5, 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 58 16.00 P 28 15.00 O 1706 8.00 N 1453 7.00 C 5450 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 339.4 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 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " 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 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1938 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 52.0% alpha, 12.0% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 82 through 91 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 157 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.510A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.258A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.695A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (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: 3.529A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.492A 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 446 through 454 removed outlier: 4.254A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.002A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 4.010A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.660A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.058A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.655A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 710 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.815A pdb=" N TYR A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 removed outlier: 3.740A pdb=" N ASN A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.632A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 4.133A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.535A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 894 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 919 through 924 removed outlier: 4.053A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.924A pdb=" N MET B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 removed outlier: 3.606A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.569A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.772A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.958A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.851A pdb=" N ARG A 33 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.293A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.412A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.412A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.523A pdb=" N LEU B 128 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 400 removed outlier: 4.480A pdb=" N PHE A 396 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 667 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.514A pdb=" N VAL A 844 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 370 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1356 1.28 - 1.41: 2434 1.41 - 1.55: 5016 1.55 - 1.68: 53 1.68 - 1.81: 87 Bond restraints: 8946 Sorted by residual: bond pdb=" C12 F86 P 24 " pdb=" N2 F86 P 24 " ideal model delta sigma weight residual 1.293 1.355 -0.062 1.00e-02 1.00e+04 3.83e+01 bond pdb=" C12 F86 P 25 " pdb=" N2 F86 P 25 " ideal model delta sigma weight residual 1.293 1.355 -0.062 1.00e-02 1.00e+04 3.80e+01 bond pdb=" C12 F86 P 23 " pdb=" N2 F86 P 23 " ideal model delta sigma weight residual 1.293 1.354 -0.061 1.00e-02 1.00e+04 3.72e+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 1.38e+01 bond pdb=" N ASP B 112 " pdb=" CA ASP B 112 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.17e+01 ... (remaining 8941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11957 1.81 - 3.62: 254 3.62 - 5.44: 42 5.44 - 7.25: 10 7.25 - 9.06: 1 Bond angle restraints: 12264 Sorted by residual: angle pdb=" CA HIS A 613 " pdb=" CB HIS A 613 " pdb=" CG HIS A 613 " ideal model delta sigma weight residual 113.80 118.83 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" C ASN B 105 " pdb=" N ILE B 106 " pdb=" CA ILE B 106 " ideal model delta sigma weight residual 122.77 117.88 4.89 1.05e+00 9.07e-01 2.16e+01 angle pdb=" CA HIS A 613 " pdb=" C HIS A 613 " pdb=" O HIS A 613 " ideal model delta sigma weight residual 121.23 117.22 4.01 1.07e+00 8.73e-01 1.41e+01 angle pdb=" C9 F86 P 23 " pdb=" C11 F86 P 23 " pdb=" N5 F86 P 23 " ideal model delta sigma weight residual 120.19 123.78 -3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" C9 F86 P 25 " pdb=" C11 F86 P 25 " pdb=" N5 F86 P 25 " ideal model delta sigma weight residual 120.19 123.77 -3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 12259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 4573 17.16 - 34.32: 523 34.32 - 51.48: 136 51.48 - 68.64: 50 68.64 - 85.80: 12 Dihedral angle restraints: 5294 sinusoidal: 2293 harmonic: 3001 Sorted by residual: dihedral pdb=" CD ARG A 116 " pdb=" NE ARG A 116 " pdb=" CZ ARG A 116 " pdb=" NH1 ARG A 116 " ideal model delta sinusoidal sigma weight residual 0.00 72.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CD ARG A 118 " pdb=" NE ARG A 118 " pdb=" CZ ARG A 118 " pdb=" NH1 ARG A 118 " ideal model delta sinusoidal sigma weight residual 0.00 44.10 -44.10 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CD ARG B 111 " pdb=" NE ARG B 111 " pdb=" CZ ARG B 111 " pdb=" NH1 ARG B 111 " ideal model delta sinusoidal sigma weight residual 0.00 -35.47 35.47 1 1.00e+01 1.00e-02 1.78e+01 ... (remaining 5291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1321 0.095 - 0.191: 69 0.191 - 0.286: 3 0.286 - 0.382: 0 0.382 - 0.477: 4 Chirality restraints: 1397 Sorted by residual: chirality pdb=" P C T 27 " pdb=" OP1 C T 27 " pdb=" OP2 C T 27 " pdb=" O5' C T 27 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" P U T 25 " pdb=" OP1 U T 25 " pdb=" OP2 U T 25 " pdb=" O5' U T 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" P U T 28 " pdb=" OP1 U T 28 " pdb=" OP2 U T 28 " pdb=" O5' U T 28 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 1394 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 116 " -1.056 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG A 116 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 116 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 116 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 116 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 118 " 0.755 9.50e-02 1.11e+02 3.38e-01 6.97e+01 pdb=" NE ARG A 118 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 118 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 118 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 118 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 111 " 0.640 9.50e-02 1.11e+02 2.87e-01 5.02e+01 pdb=" NE ARG B 111 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B 111 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 111 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 111 " 0.021 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 317 2.72 - 3.26: 8389 3.26 - 3.81: 13768 3.81 - 4.35: 18256 4.35 - 4.90: 29666 Nonbonded interactions: 70396 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.171 3.040 nonbonded pdb=" O ILE A 847 " pdb=" OG1 THR A 850 " model vdw 2.195 3.040 nonbonded pdb=" O ASN A 705 " pdb=" OG SER A 709 " model vdw 2.241 3.040 nonbonded pdb=" O PRO A 612 " pdb=" ND1 HIS A 613 " model vdw 2.296 3.120 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.313 3.040 ... (remaining 70391 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: 0.300 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: 0.020 Set scattering table: 0.040 Process input model: 12.080 Find NCS groups from input model: 0.040 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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 : 0.004 0.063 8957 Z= 0.264 Angle : 0.613 9.060 12270 Z= 0.376 Chirality : 0.050 0.477 1397 Planarity : 0.017 0.473 1460 Dihedral : 16.460 85.802 3356 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.24 % Allowed : 14.45 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.02 (0.25), residues: 999 helix: -0.77 (0.22), residues: 454 sheet: 0.07 (0.55), residues: 97 loop : -0.57 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.022 0.001 TYR A 788 PHE 0.007 0.001 PHE A 694 TRP 0.006 0.001 TRP A 800 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8946) covalent geometry : angle 0.61282 (12264) hydrogen bonds : bond 0.28930 ( 375) hydrogen bonds : angle 7.90819 ( 1054) metal coordination : bond 0.01221 ( 8) metal coordination : angle 1.37586 ( 6) Misc. bond : bond 0.04631 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.3772 (OUTLIER) cc_final: 0.2856 (mm-30) REVERT: A 196 MET cc_start: 0.6669 (ttp) cc_final: 0.5985 (ttp) REVERT: A 265 TYR cc_start: 0.7578 (m-80) cc_final: 0.7208 (m-80) REVERT: A 629 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8526 (tpt) REVERT: A 796 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: A 876 GLU cc_start: 0.7657 (tt0) cc_final: 0.7375 (tt0) REVERT: B 104 ASN cc_start: 0.5480 (OUTLIER) cc_final: 0.5240 (t0) outliers start: 20 outliers final: 6 residues processed: 106 average time/residue: 0.5501 time to fit residues: 62.6632 Evaluate side-chains 98 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 111 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 256 HIS A 497 ASN A 628 ASN B 108 ASN B 158 GLN C 31 GLN C 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.188492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149204 restraints weight = 10166.489| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.81 r_work: 0.3667 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8957 Z= 0.130 Angle : 0.535 8.158 12270 Z= 0.283 Chirality : 0.041 0.132 1397 Planarity : 0.004 0.043 1460 Dihedral : 12.172 86.859 1502 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.25 % Allowed : 13.55 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.22 (0.25), residues: 999 helix: 0.38 (0.24), residues: 460 sheet: 0.23 (0.53), residues: 87 loop : -0.67 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.013 0.001 TYR A 867 PHE 0.014 0.001 PHE A 694 TRP 0.008 0.001 TRP A 598 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8946) covalent geometry : angle 0.53377 (12264) hydrogen bonds : bond 0.05250 ( 375) hydrogen bonds : angle 4.79740 ( 1054) metal coordination : bond 0.01480 ( 8) metal coordination : angle 1.48677 ( 6) Misc. bond : bond 0.00072 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.2695 (mm-30) REVERT: A 265 TYR cc_start: 0.7681 (m-80) cc_final: 0.7392 (m-80) REVERT: A 608 ASP cc_start: 0.7994 (m-30) cc_final: 0.7746 (t70) REVERT: A 622 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7194 (t) REVERT: A 796 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: A 815 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: A 876 GLU cc_start: 0.7543 (tt0) cc_final: 0.7215 (tt0) REVERT: B 94 MET cc_start: 0.6220 (ttm) cc_final: 0.5914 (ttp) REVERT: B 104 ASN cc_start: 0.5808 (OUTLIER) cc_final: 0.5385 (t0) outliers start: 29 outliers final: 12 residues processed: 114 average time/residue: 0.4749 time to fit residues: 58.7882 Evaluate side-chains 106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 892 HIS C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.185918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146275 restraints weight = 10135.565| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.80 r_work: 0.3636 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8957 Z= 0.162 Angle : 0.544 8.979 12270 Z= 0.287 Chirality : 0.041 0.144 1397 Planarity : 0.004 0.036 1460 Dihedral : 11.974 89.611 1493 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.70 % Allowed : 15.01 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 999 helix: 0.47 (0.24), residues: 472 sheet: -0.21 (0.50), residues: 100 loop : -0.79 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 640 TYR 0.016 0.002 TYR A 867 PHE 0.016 0.002 PHE A 694 TRP 0.009 0.001 TRP A 800 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8946) covalent geometry : angle 0.54266 (12264) hydrogen bonds : bond 0.05394 ( 375) hydrogen bonds : angle 4.59610 ( 1054) metal coordination : bond 0.02088 ( 8) metal coordination : angle 2.06375 ( 6) Misc. bond : bond 0.00136 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.4099 (OUTLIER) cc_final: 0.2729 (mm-30) REVERT: A 608 ASP cc_start: 0.7962 (m-30) cc_final: 0.7754 (t70) REVERT: A 622 CYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7178 (t) REVERT: A 629 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8508 (tpt) REVERT: A 796 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 876 GLU cc_start: 0.7564 (tt0) cc_final: 0.7197 (tt0) outliers start: 33 outliers final: 13 residues processed: 108 average time/residue: 0.5051 time to fit residues: 59.0089 Evaluate side-chains 107 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 497 ASN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.189864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151880 restraints weight = 10244.283| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.84 r_work: 0.3685 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8957 Z= 0.103 Angle : 0.465 7.910 12270 Z= 0.245 Chirality : 0.039 0.169 1397 Planarity : 0.003 0.035 1460 Dihedral : 11.466 90.991 1488 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.02 % Allowed : 16.35 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.26), residues: 999 helix: 0.81 (0.25), residues: 464 sheet: -0.43 (0.48), residues: 99 loop : -0.63 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.015 0.001 TYR A 867 PHE 0.011 0.001 PHE A 652 TRP 0.006 0.001 TRP A 598 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8946) covalent geometry : angle 0.46375 (12264) hydrogen bonds : bond 0.03924 ( 375) hydrogen bonds : angle 4.28893 ( 1054) metal coordination : bond 0.01000 ( 8) metal coordination : angle 1.34951 ( 6) Misc. bond : bond 0.00042 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.3940 (OUTLIER) cc_final: 0.2515 (mm-30) REVERT: A 265 TYR cc_start: 0.7620 (m-80) cc_final: 0.7270 (m-80) REVERT: A 608 ASP cc_start: 0.7988 (m-30) cc_final: 0.7756 (t70) REVERT: A 622 CYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7091 (t) REVERT: A 629 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8557 (tpt) REVERT: A 658 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: A 666 MET cc_start: 0.7991 (mmt) cc_final: 0.7627 (mpp) REVERT: A 796 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 876 GLU cc_start: 0.7505 (tt0) cc_final: 0.7197 (tt0) outliers start: 27 outliers final: 10 residues processed: 108 average time/residue: 0.4724 time to fit residues: 55.4997 Evaluate side-chains 104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 796 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 34 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 497 ASN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.192202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152425 restraints weight = 10138.467| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.83 r_work: 0.3698 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8957 Z= 0.090 Angle : 0.439 7.507 12270 Z= 0.231 Chirality : 0.038 0.143 1397 Planarity : 0.003 0.043 1460 Dihedral : 11.245 91.628 1486 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.25 % Allowed : 16.35 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.27), residues: 999 helix: 1.17 (0.25), residues: 454 sheet: -0.35 (0.48), residues: 99 loop : -0.53 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 858 TYR 0.015 0.001 TYR A 867 PHE 0.010 0.001 PHE A 652 TRP 0.006 0.001 TRP A 598 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 8946) covalent geometry : angle 0.43829 (12264) hydrogen bonds : bond 0.03393 ( 375) hydrogen bonds : angle 4.06280 ( 1054) metal coordination : bond 0.00662 ( 8) metal coordination : angle 1.19316 ( 6) Misc. bond : bond 0.00029 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.348 Fit side-chains REVERT: A 83 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.2678 (mm-30) REVERT: A 265 TYR cc_start: 0.7633 (m-80) cc_final: 0.7297 (m-80) REVERT: A 401 LEU cc_start: 0.8600 (mp) cc_final: 0.8316 (mt) REVERT: A 622 CYS cc_start: 0.7589 (t) cc_final: 0.7025 (t) REVERT: A 629 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8451 (tpt) REVERT: A 658 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: A 666 MET cc_start: 0.7938 (mmt) cc_final: 0.7599 (mpp) REVERT: A 796 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: B 185 ILE cc_start: 0.7745 (mp) cc_final: 0.7275 (tt) outliers start: 29 outliers final: 13 residues processed: 117 average time/residue: 0.4612 time to fit residues: 58.5707 Evaluate side-chains 107 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.188787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148839 restraints weight = 10147.497| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.82 r_work: 0.3660 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8957 Z= 0.133 Angle : 0.488 8.857 12270 Z= 0.257 Chirality : 0.040 0.155 1397 Planarity : 0.003 0.043 1460 Dihedral : 11.288 91.005 1486 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.14 % Allowed : 16.57 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.26), residues: 999 helix: 1.03 (0.25), residues: 457 sheet: -0.52 (0.47), residues: 112 loop : -0.64 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.015 0.002 TYR A 867 PHE 0.014 0.001 PHE A 694 TRP 0.025 0.002 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8946) covalent geometry : angle 0.48661 (12264) hydrogen bonds : bond 0.04178 ( 375) hydrogen bonds : angle 4.20080 ( 1054) metal coordination : bond 0.01468 ( 8) metal coordination : angle 1.64870 ( 6) Misc. bond : bond 0.00072 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.351 Fit side-chains REVERT: A 83 GLU cc_start: 0.4066 (OUTLIER) cc_final: 0.2472 (mm-30) REVERT: A 265 TYR cc_start: 0.7650 (m-80) cc_final: 0.7307 (m-80) REVERT: A 622 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7101 (t) REVERT: A 629 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8496 (tpt) REVERT: A 658 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: A 796 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: A 815 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: C 52 MET cc_start: 0.5590 (tmm) cc_final: 0.5254 (mmm) REVERT: C 62 MET cc_start: 0.3129 (OUTLIER) cc_final: 0.2848 (mpt) outliers start: 37 outliers final: 19 residues processed: 113 average time/residue: 0.4158 time to fit residues: 51.4530 Evaluate side-chains 113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 62 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 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 497 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146318 restraints weight = 10180.881| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.80 r_work: 0.3630 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8957 Z= 0.165 Angle : 0.544 8.766 12270 Z= 0.287 Chirality : 0.042 0.160 1397 Planarity : 0.004 0.051 1460 Dihedral : 11.431 90.291 1486 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.37 % Allowed : 16.69 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.16 (0.26), residues: 999 helix: 0.73 (0.25), residues: 461 sheet: -0.32 (0.49), residues: 100 loop : -0.89 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 858 TYR 0.018 0.002 TYR A 867 PHE 0.017 0.002 PHE A 741 TRP 0.018 0.002 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8946) covalent geometry : angle 0.54267 (12264) hydrogen bonds : bond 0.04874 ( 375) hydrogen bonds : angle 4.41708 ( 1054) metal coordination : bond 0.01975 ( 8) metal coordination : angle 2.07808 ( 6) Misc. bond : bond 0.00092 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.265 Fit side-chains REVERT: A 83 GLU cc_start: 0.4264 (OUTLIER) cc_final: 0.2466 (mm-30) REVERT: A 527 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 629 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8533 (tpt) REVERT: A 640 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.5538 (mpt-90) REVERT: A 760 ASP cc_start: 0.7667 (m-30) cc_final: 0.7413 (m-30) REVERT: A 796 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: C 52 MET cc_start: 0.5680 (tmm) cc_final: 0.5374 (mmm) REVERT: C 62 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.3160 (mpt) outliers start: 39 outliers final: 23 residues processed: 114 average time/residue: 0.4619 time to fit residues: 57.2889 Evaluate side-chains 116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 640 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 62 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 0.0270 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149811 restraints weight = 9997.267| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.79 r_work: 0.3673 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8957 Z= 0.103 Angle : 0.471 9.037 12270 Z= 0.249 Chirality : 0.039 0.169 1397 Planarity : 0.003 0.044 1460 Dihedral : 11.323 90.692 1486 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.14 % Allowed : 18.37 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.10 (0.26), residues: 999 helix: 0.95 (0.25), residues: 462 sheet: -0.39 (0.49), residues: 99 loop : -0.70 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.017 0.001 TYR A 867 PHE 0.011 0.001 PHE A 652 TRP 0.017 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8946) covalent geometry : angle 0.47013 (12264) hydrogen bonds : bond 0.03741 ( 375) hydrogen bonds : angle 4.20125 ( 1054) metal coordination : bond 0.00859 ( 8) metal coordination : angle 1.21979 ( 6) Misc. bond : bond 0.00042 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.328 Fit side-chains REVERT: A 265 TYR cc_start: 0.7558 (m-10) cc_final: 0.7232 (m-80) REVERT: A 527 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 629 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8506 (tpt) REVERT: A 658 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 796 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: C 52 MET cc_start: 0.5581 (tmm) cc_final: 0.5249 (mmm) outliers start: 28 outliers final: 16 residues processed: 107 average time/residue: 0.4621 time to fit residues: 53.8494 Evaluate side-chains 106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 833 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 875 GLN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.190006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150216 restraints weight = 9995.372| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.79 r_work: 0.3678 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8957 Z= 0.105 Angle : 0.487 8.743 12270 Z= 0.256 Chirality : 0.039 0.167 1397 Planarity : 0.003 0.041 1460 Dihedral : 11.174 91.196 1483 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.58 % Allowed : 19.15 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.26), residues: 999 helix: 1.01 (0.25), residues: 462 sheet: -0.36 (0.48), residues: 99 loop : -0.67 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.018 0.001 TYR A 129 PHE 0.011 0.001 PHE A 694 TRP 0.015 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8946) covalent geometry : angle 0.48589 (12264) hydrogen bonds : bond 0.03739 ( 375) hydrogen bonds : angle 4.15910 ( 1054) metal coordination : bond 0.00911 ( 8) metal coordination : angle 1.29204 ( 6) Misc. bond : bond 0.00043 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.332 Fit side-chains REVERT: A 265 TYR cc_start: 0.7553 (m-10) cc_final: 0.7225 (m-80) REVERT: A 527 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7725 (tt) REVERT: A 629 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8501 (tpt) REVERT: A 658 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 760 ASP cc_start: 0.7589 (m-30) cc_final: 0.7378 (m-30) REVERT: A 796 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: C 52 MET cc_start: 0.5503 (tmm) cc_final: 0.5172 (mmm) outliers start: 23 outliers final: 17 residues processed: 104 average time/residue: 0.4591 time to fit residues: 51.9927 Evaluate side-chains 106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 833 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 46 optimal weight: 0.0870 chunk 96 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.186740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146654 restraints weight = 10144.876| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.79 r_work: 0.3624 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8957 Z= 0.165 Angle : 0.555 9.086 12270 Z= 0.291 Chirality : 0.042 0.193 1397 Planarity : 0.004 0.044 1460 Dihedral : 11.257 90.940 1483 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.91 % Allowed : 19.37 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 999 helix: 0.78 (0.25), residues: 461 sheet: -0.31 (0.49), residues: 100 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 858 TYR 0.022 0.002 TYR A 129 PHE 0.016 0.002 PHE A 694 TRP 0.013 0.002 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8946) covalent geometry : angle 0.55355 (12264) hydrogen bonds : bond 0.04687 ( 375) hydrogen bonds : angle 4.38767 ( 1054) metal coordination : bond 0.01741 ( 8) metal coordination : angle 1.86122 ( 6) Misc. bond : bond 0.00093 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.356 Fit side-chains REVERT: A 265 TYR cc_start: 0.7571 (m-10) cc_final: 0.7241 (m-80) REVERT: A 527 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7719 (tt) REVERT: A 629 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8526 (tpt) REVERT: A 760 ASP cc_start: 0.7659 (m-30) cc_final: 0.7434 (m-30) REVERT: A 796 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: C 52 MET cc_start: 0.5570 (tmm) cc_final: 0.5265 (mmm) outliers start: 26 outliers final: 20 residues processed: 102 average time/residue: 0.4691 time to fit residues: 52.1650 Evaluate side-chains 108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 0.0070 chunk 16 optimal weight: 20.0000 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.191223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151390 restraints weight = 10047.550| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.80 r_work: 0.3694 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8957 Z= 0.096 Angle : 0.476 9.201 12270 Z= 0.252 Chirality : 0.039 0.191 1397 Planarity : 0.003 0.043 1460 Dihedral : 11.142 91.114 1483 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.90 % Allowed : 19.93 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 999 helix: 1.05 (0.25), residues: 460 sheet: -0.35 (0.48), residues: 99 loop : -0.58 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 858 TYR 0.016 0.001 TYR A 129 PHE 0.011 0.001 PHE A 652 TRP 0.015 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8946) covalent geometry : angle 0.47588 (12264) hydrogen bonds : bond 0.03410 ( 375) hydrogen bonds : angle 4.15138 ( 1054) metal coordination : bond 0.00578 ( 8) metal coordination : angle 1.18873 ( 6) Misc. bond : bond 0.00035 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.34 seconds wall clock time: 56 minutes 26.14 seconds (3386.14 seconds total)