Starting phenix.real_space_refine on Sat Oct 11 04:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rme_19359/10_2025/8rme_19359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rme_19359/10_2025/8rme_19359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rme_19359/10_2025/8rme_19359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rme_19359/10_2025/8rme_19359.map" model { file = "/net/cci-nas-00/data/ceres_data/8rme_19359/10_2025/8rme_19359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rme_19359/10_2025/8rme_19359.cif" } resolution = 2.49 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= 0.001 sd= 0.038 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 Fe 2 7.16 5 P 4 5.49 5 S 59 5.16 5 C 7287 2.51 5 N 2016 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11762 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3140 Classifications: {'peptide': 401} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 381} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "D" Number of atoms: 939 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} bond proxies already assigned to first conformer: 927 Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 3082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 3057 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 392, 3057 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3085 Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 939 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Conformer: "D" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} bond proxies already assigned to first conformer: 927 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2529 SG CYS A 381 33.522 42.781 65.744 1.00102.83 S ATOM 4296 SG CYS D 95 33.489 39.567 63.999 1.00 79.99 S ATOM 8808 SG CYS E 381 73.719 95.939 65.659 1.00 94.31 S ATOM 11074 SG CYS H 95 73.374 98.637 63.467 1.00 67.25 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ATYR D 35 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR D 35 " occ=0.45 residue: pdb=" N AASN E 83 " occ=0.46 ... (14 atoms not shown) pdb=" ND2BASN E 83 " occ=0.54 residue: pdb=" N AARG E 321 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG E 321 " occ=0.37 residue: pdb=" N ACYS E 426 " occ=0.26 ... (10 atoms not shown) pdb=" SG BCYS E 426 " occ=0.74 residue: pdb=" N BTYR H 35 " occ=0.82 ... (22 atoms not shown) pdb=" OH DTYR H 35 " occ=0.18 Time building chain proxies: 4.18, per 1000 atoms: 0.36 Number of scatterers: 11762 At special positions: 0 Unit cell: (107.64, 142.416, 104.328, 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) Fe 2 26.01 S 59 16.00 P 4 15.00 O 2394 8.00 N 2016 7.00 C 7287 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 792.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2750 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 55.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 126 through 142 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.541A pdb=" N ILE A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 297 through 337 removed outlier: 5.655A pdb=" N GLU A 316 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.002A pdb=" N HIS A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.587A pdb=" N ALA A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A 403 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 Processing helix chain 'A' and resid 437 through 445 removed outlier: 3.738A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.507A pdb=" N SER A 451 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 25 through 43 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.673A pdb=" N ASN B 85 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 45 removed outlier: 4.084A pdb=" N HIS D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 109 Processing helix chain 'D' and resid 113 through 119 removed outlier: 4.062A pdb=" N THR D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 135 through 157 removed outlier: 3.941A pdb=" N SER D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 113 Processing helix chain 'I' and resid 181 through 195 Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 36 through 52 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'E' and resid 70 through 83 Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 93 through 115 removed outlier: 3.578A pdb=" N ILE E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 126 through 142 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 214 through 225 Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 297 through 337 removed outlier: 5.449A pdb=" N GLU E 316 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 removed outlier: 3.859A pdb=" N HIS E 349 " --> pdb=" O PRO E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 370 Processing helix chain 'E' and resid 379 through 383 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 415 through 437 Processing helix chain 'E' and resid 437 through 445 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 25 through 43 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 36 through 51 Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'G' and resid 65 through 76 Processing helix chain 'H' and resid 36 through 45 Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 121 through 130 removed outlier: 3.512A pdb=" N ILE H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 135 through 157 removed outlier: 4.032A pdb=" N SER H 139 " --> pdb=" O LYS H 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.846A pdb=" N LEU A 59 " --> pdb=" O ALA A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.855A pdb=" N SER A 198 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N HIS A 230 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 200 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ASP A 232 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS A 148 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 200 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 150 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 149 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU A 176 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 151 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 342 removed outlier: 3.666A pdb=" N SER A 376 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 65 removed outlier: 3.826A pdb=" N ASP D 87 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.724A pdb=" N VAL I 144 " --> pdb=" O SER I 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.830A pdb=" N LEU E 59 " --> pdb=" O ALA E 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.818A pdb=" N SER E 198 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N HIS E 230 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 200 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP E 232 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N HIS E 148 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL E 200 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE E 150 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 149 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR E 151 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 340 through 342 removed outlier: 3.678A pdb=" N SER E 376 " --> pdb=" O ARG E 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 59 through 65 removed outlier: 3.563A pdb=" N ASP H 87 " --> pdb=" O GLN H 78 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1982 1.30 - 1.43: 2876 1.43 - 1.56: 6834 1.56 - 1.69: 5 1.69 - 1.82: 95 Bond restraints: 11792 Sorted by residual: bond pdb=" NZ LLP E 258 " pdb=" C4' LLP E 258 " ideal model delta sigma weight residual 1.273 1.430 -0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" NZ LLP A 258 " pdb=" C4' LLP A 258 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" OP4 LLP A 258 " pdb=" P LLP A 258 " ideal model delta sigma weight residual 1.726 1.609 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" OP4 LLP E 258 " pdb=" P LLP E 258 " ideal model delta sigma weight residual 1.726 1.610 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C PRO E 71 " pdb=" O PRO E 71 " ideal model delta sigma weight residual 1.238 1.179 0.058 1.24e-02 6.50e+03 2.21e+01 ... (remaining 11787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 15821 4.11 - 8.21: 101 8.21 - 12.32: 3 12.32 - 16.43: 0 16.43 - 20.54: 1 Bond angle restraints: 15926 Sorted by residual: angle pdb=" NZ LLP E 258 " pdb=" C4' LLP E 258 " pdb=" C4 LLP E 258 " ideal model delta sigma weight residual 120.09 99.55 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" CA ARG E 273 " pdb=" C ARG E 273 " pdb=" O ARG E 273 " ideal model delta sigma weight residual 120.63 113.72 6.91 1.05e+00 9.07e-01 4.33e+01 angle pdb=" CA ARG E 273 " pdb=" C ARG E 273 " pdb=" N PRO E 274 " ideal model delta sigma weight residual 118.05 123.97 -5.92 9.50e-01 1.11e+00 3.89e+01 angle pdb=" N LEU D 155 " pdb=" CA LEU D 155 " pdb=" C LEU D 155 " ideal model delta sigma weight residual 111.07 117.55 -6.48 1.07e+00 8.73e-01 3.67e+01 angle pdb=" N GLU A 435 " pdb=" CA GLU A 435 " pdb=" C GLU A 435 " ideal model delta sigma weight residual 112.89 105.46 7.43 1.24e+00 6.50e-01 3.59e+01 ... (remaining 15921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 6854 32.67 - 65.33: 330 65.33 - 98.00: 44 98.00 - 130.67: 1 130.67 - 163.33: 8 Dihedral angle restraints: 7237 sinusoidal: 2966 harmonic: 4271 Sorted by residual: dihedral pdb=" C37 8Q1 C 101 " pdb=" C38 8Q1 C 101 " pdb=" C39 8Q1 C 101 " pdb=" O40 8Q1 C 101 " ideal model delta sinusoidal sigma weight residual -114.72 48.61 -163.33 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C37 8Q1 C 101 " pdb=" C38 8Q1 C 101 " pdb=" C39 8Q1 C 101 " pdb=" N41 8Q1 C 101 " ideal model delta sinusoidal sigma weight residual 64.60 -133.17 -162.23 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C39 8Q1 C 101 " pdb=" C42 8Q1 C 101 " pdb=" N41 8Q1 C 101 " pdb=" C43 8Q1 C 101 " ideal model delta sinusoidal sigma weight residual 89.93 -66.27 156.20 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 7234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1451 0.062 - 0.123: 265 0.123 - 0.185: 58 0.185 - 0.246: 21 0.246 - 0.308: 6 Chirality restraints: 1801 Sorted by residual: chirality pdb=" CA ASP A 339 " pdb=" N ASP A 339 " pdb=" C ASP A 339 " pdb=" CB ASP A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ASP E 339 " pdb=" N ASP E 339 " pdb=" C ASP E 339 " pdb=" CB ASP E 339 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL E 73 " pdb=" CA VAL E 73 " pdb=" CG1 VAL E 73 " pdb=" CG2 VAL E 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1798 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 258 " 0.010 2.00e-02 2.50e+03 2.93e-01 8.61e+02 pdb=" NZ LLP A 258 " 0.231 2.00e-02 2.50e+03 pdb=" C4 LLP A 258 " 0.241 2.00e-02 2.50e+03 pdb=" C4' LLP A 258 " -0.482 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 8Q1 G 101 " -0.069 2.00e-02 2.50e+03 7.98e-02 7.97e+01 pdb=" C34 8Q1 G 101 " 0.014 2.00e-02 2.50e+03 pdb=" C37 8Q1 G 101 " -0.097 2.00e-02 2.50e+03 pdb=" N36 8Q1 G 101 " 0.131 2.00e-02 2.50e+03 pdb=" O35 8Q1 G 101 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 G 101 " 0.053 2.00e-02 2.50e+03 5.75e-02 4.14e+01 pdb=" C39 8Q1 G 101 " -0.020 2.00e-02 2.50e+03 pdb=" C42 8Q1 G 101 " 0.070 2.00e-02 2.50e+03 pdb=" N41 8Q1 G 101 " -0.091 2.00e-02 2.50e+03 pdb=" O40 8Q1 G 101 " -0.013 2.00e-02 2.50e+03 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 159 2.64 - 3.20: 10352 3.20 - 3.77: 19118 3.77 - 4.33: 28302 4.33 - 4.90: 44649 Nonbonded interactions: 102580 Sorted by model distance: nonbonded pdb=" OD1 ASP D 71 " pdb="FE FE2 D 201 " model vdw 2.073 3.000 nonbonded pdb=" O SER E 365 " pdb=" OH TYR H 43 " model vdw 2.086 3.040 nonbonded pdb=" OD2 ASP D 71 " pdb="FE FE2 D 201 " model vdw 2.140 3.000 nonbonded pdb=" OD1 ASP H 71 " pdb="FE FE2 H 201 " model vdw 2.192 3.000 nonbonded pdb=" OE1 GLN E 312 " pdb=" O HOH E 601 " model vdw 2.204 3.040 ... (remaining 102575 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 425 or resid 427 through 447)) selection = (chain 'E' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 382 or resid 384 through 425 or resid 427 through 447)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 36 through 201) selection = (chain 'H' and resid 36 through 201) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.157 11794 Z= 0.389 Angle : 0.859 20.537 15926 Z= 0.561 Chirality : 0.057 0.308 1801 Planarity : 0.008 0.293 2049 Dihedral : 19.047 163.335 4487 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.67 % Allowed : 18.82 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.42 (0.22), residues: 1451 helix: 0.81 (0.18), residues: 794 sheet: 0.18 (0.38), residues: 203 loop : -0.45 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 292 TYR 0.016 0.002 TYR A 350 PHE 0.020 0.002 PHE F 40 TRP 0.015 0.002 TRP E 440 HIS 0.017 0.002 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00641 (11792) covalent geometry : angle 0.85928 (15926) hydrogen bonds : bond 0.16070 ( 641) hydrogen bonds : angle 5.97382 ( 1871) Misc. bond : bond 0.03136 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7549 (mtm110) cc_final: 0.6723 (pmt170) REVERT: A 226 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7991 (mtmm) REVERT: A 321 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7771 (mtp180) REVERT: A 347 LYS cc_start: 0.8240 (mttm) cc_final: 0.7913 (mtmt) REVERT: A 417 GLU cc_start: 0.7621 (tt0) cc_final: 0.7250 (mp0) REVERT: D 118 LEU cc_start: 0.7788 (mt) cc_final: 0.7429 (mp) REVERT: I 148 GLN cc_start: 0.8206 (tp-100) cc_final: 0.8000 (mm-40) REVERT: E 91 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7884 (mtt-85) REVERT: E 144 SER cc_start: 0.8637 (p) cc_final: 0.8402 (p) REVERT: E 145 ARG cc_start: 0.7082 (mtm110) cc_final: 0.6514 (pmt170) REVERT: E 275 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.7228 (tpt-90) REVERT: E 327 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7264 (mt-10) REVERT: E 417 GLU cc_start: 0.7817 (tt0) cc_final: 0.7296 (mp0) REVERT: F 18 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7170 (mtt-85) REVERT: F 42 GLU cc_start: 0.7686 (tt0) cc_final: 0.7148 (mt-10) REVERT: F 51 GLU cc_start: 0.7516 (tp30) cc_final: 0.7174 (tm-30) REVERT: F 71 HIS cc_start: 0.7721 (t-90) cc_final: 0.7452 (t-90) REVERT: H 157 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5910 (mt0) outliers start: 19 outliers final: 9 residues processed: 178 average time/residue: 0.7718 time to fit residues: 146.1802 Evaluate side-chains 155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 157 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN E 179 GLN E 194 GLN E 207 ASN E 245 ASN E 348 HIS G 20 GLN G 25 ASN H 157 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089727 restraints weight = 33104.461| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.06 r_work: 0.2900 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11794 Z= 0.126 Angle : 0.500 7.431 15926 Z= 0.266 Chirality : 0.042 0.171 1801 Planarity : 0.004 0.051 2049 Dihedral : 11.192 171.277 1693 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 18.02 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.28 (0.22), residues: 1451 helix: 1.64 (0.19), residues: 796 sheet: 0.35 (0.38), residues: 203 loop : -0.23 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 89 TYR 0.013 0.002 TYR E 80 PHE 0.010 0.001 PHE H 93 TRP 0.009 0.001 TRP H 108 HIS 0.004 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00276 (11792) covalent geometry : angle 0.49974 (15926) hydrogen bonds : bond 0.04913 ( 641) hydrogen bonds : angle 4.48106 ( 1871) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8059 (mtmm) REVERT: A 347 LYS cc_start: 0.8376 (mttm) cc_final: 0.7965 (mtmt) REVERT: A 417 GLU cc_start: 0.7692 (tt0) cc_final: 0.7172 (mp0) REVERT: B 71 HIS cc_start: 0.7946 (t-90) cc_final: 0.7669 (t-170) REVERT: D 89 ARG cc_start: 0.7758 (mmt90) cc_final: 0.6735 (mmp80) REVERT: E 91 ARG cc_start: 0.8644 (mtp-110) cc_final: 0.8042 (mtt-85) REVERT: E 144 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8339 (p) REVERT: E 145 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6541 (pmt170) REVERT: E 247 MET cc_start: 0.8876 (mtt) cc_final: 0.8465 (mtt) REVERT: E 273 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7920 (ttt180) REVERT: E 275 ARG cc_start: 0.7885 (tpp-160) cc_final: 0.7294 (tpt-90) REVERT: E 320 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7541 (mtpm) REVERT: E 327 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7327 (mt-10) REVERT: E 417 GLU cc_start: 0.7891 (tt0) cc_final: 0.7187 (mp0) REVERT: F 18 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7163 (mtm-85) REVERT: F 71 HIS cc_start: 0.7684 (t-90) cc_final: 0.7434 (t-90) REVERT: H 118 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7641 (mm) outliers start: 25 outliers final: 8 residues processed: 172 average time/residue: 0.7923 time to fit residues: 145.0894 Evaluate side-chains 153 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 130 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091617 restraints weight = 43968.403| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.67 r_work: 0.2914 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11794 Z= 0.098 Angle : 0.447 7.398 15926 Z= 0.237 Chirality : 0.041 0.156 1801 Planarity : 0.003 0.047 2049 Dihedral : 8.810 147.172 1675 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.91 % Allowed : 18.90 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.66 (0.23), residues: 1451 helix: 1.97 (0.19), residues: 797 sheet: 0.51 (0.39), residues: 201 loop : -0.12 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 89 TYR 0.011 0.001 TYR E 80 PHE 0.010 0.001 PHE D 93 TRP 0.006 0.001 TRP H 108 HIS 0.005 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00206 (11792) covalent geometry : angle 0.44661 (15926) hydrogen bonds : bond 0.04101 ( 641) hydrogen bonds : angle 4.18910 ( 1871) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7787 (mtm110) cc_final: 0.6518 (pmt170) REVERT: A 226 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8057 (mtmm) REVERT: A 291 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: A 347 LYS cc_start: 0.8306 (mttm) cc_final: 0.7879 (mtmt) REVERT: A 417 GLU cc_start: 0.7725 (tt0) cc_final: 0.7167 (mp0) REVERT: B 71 HIS cc_start: 0.8121 (t-90) cc_final: 0.7796 (t-90) REVERT: D 89 ARG cc_start: 0.7665 (mmt90) cc_final: 0.6769 (mtp85) REVERT: I 164 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8331 (mmtp) REVERT: E 145 ARG cc_start: 0.7392 (mtm110) cc_final: 0.6593 (pmt170) REVERT: E 247 MET cc_start: 0.8866 (mtt) cc_final: 0.8443 (mtt) REVERT: E 273 ARG cc_start: 0.8164 (ttt90) cc_final: 0.7748 (ttt90) REVERT: E 275 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7353 (tpt-90) REVERT: E 320 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7504 (mtpm) REVERT: E 417 GLU cc_start: 0.7882 (tt0) cc_final: 0.7120 (mp0) REVERT: F 71 HIS cc_start: 0.7922 (t-90) cc_final: 0.7639 (t-90) REVERT: H 37 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7211 (tmtm) REVERT: H 118 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7203 (mm) outliers start: 22 outliers final: 6 residues processed: 163 average time/residue: 0.7860 time to fit residues: 136.3549 Evaluate side-chains 152 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 HIS I 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090094 restraints weight = 32536.575| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.04 r_work: 0.2911 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.002 0.027 11794 Z= 0.112 Angle : 0.454 6.808 15926 Z= 0.241 Chirality : 0.042 0.142 1801 Planarity : 0.003 0.044 2049 Dihedral : 8.124 127.287 1674 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.15 % Allowed : 17.94 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.75 (0.23), residues: 1451 helix: 2.05 (0.19), residues: 799 sheet: 0.53 (0.39), residues: 201 loop : -0.10 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.013 0.002 TYR A 260 PHE 0.008 0.001 PHE H 93 TRP 0.006 0.001 TRP H 108 HIS 0.004 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00248 (11792) covalent geometry : angle 0.45406 (15926) hydrogen bonds : bond 0.04410 ( 641) hydrogen bonds : angle 4.18135 ( 1871) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 145 ARG cc_start: 0.7800 (mtm110) cc_final: 0.6576 (pmt170) REVERT: A 226 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7798 (mptp) REVERT: A 347 LYS cc_start: 0.8311 (mttm) cc_final: 0.7898 (mtmt) REVERT: A 362 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: A 364 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: A 417 GLU cc_start: 0.7713 (tt0) cc_final: 0.7161 (mp0) REVERT: B 18 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7635 (mtt90) REVERT: D 89 ARG cc_start: 0.7667 (mmt90) cc_final: 0.6786 (mtp85) REVERT: E 145 ARG cc_start: 0.7458 (mtm110) cc_final: 0.6660 (pmt170) REVERT: E 247 MET cc_start: 0.8869 (mtt) cc_final: 0.8451 (mtt) REVERT: E 273 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7787 (ttt90) REVERT: E 275 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7444 (ttt-90) REVERT: E 417 GLU cc_start: 0.7895 (tt0) cc_final: 0.7169 (mp0) REVERT: F 71 HIS cc_start: 0.7890 (t-90) cc_final: 0.7666 (t-90) REVERT: H 118 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7204 (mm) outliers start: 25 outliers final: 9 residues processed: 159 average time/residue: 0.8097 time to fit residues: 136.8374 Evaluate side-chains 150 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN E 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091222 restraints weight = 37922.702| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.05 r_work: 0.2933 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11794 Z= 0.098 Angle : 0.436 7.080 15926 Z= 0.230 Chirality : 0.041 0.140 1801 Planarity : 0.003 0.042 2049 Dihedral : 6.994 93.001 1674 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.63 % Allowed : 18.34 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.83 (0.23), residues: 1451 helix: 2.15 (0.19), residues: 799 sheet: 0.42 (0.39), residues: 204 loop : -0.03 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 89 TYR 0.011 0.001 TYR E 80 PHE 0.007 0.001 PHE H 93 TRP 0.006 0.001 TRP H 108 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00209 (11792) covalent geometry : angle 0.43637 (15926) hydrogen bonds : bond 0.03999 ( 641) hydrogen bonds : angle 4.07951 ( 1871) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: A 145 ARG cc_start: 0.7586 (mtm110) cc_final: 0.6261 (pmt170) REVERT: A 226 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7534 (mptp) REVERT: A 291 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8101 (mtm) REVERT: A 347 LYS cc_start: 0.8048 (mttm) cc_final: 0.7586 (mtmt) REVERT: A 362 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6014 (tm-30) REVERT: A 364 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6391 (tt0) REVERT: A 417 GLU cc_start: 0.7477 (tt0) cc_final: 0.6757 (mp0) REVERT: B 18 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7226 (mtt90) REVERT: D 89 ARG cc_start: 0.7386 (mmt90) cc_final: 0.6446 (mtp85) REVERT: E 145 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6373 (pmt170) REVERT: E 247 MET cc_start: 0.8644 (mtt) cc_final: 0.8204 (mtt) REVERT: E 273 ARG cc_start: 0.7919 (ttt90) cc_final: 0.7539 (ttt90) REVERT: E 275 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7171 (ttt-90) REVERT: E 417 GLU cc_start: 0.7598 (tt0) cc_final: 0.6766 (mp0) REVERT: F 42 GLU cc_start: 0.7534 (tt0) cc_final: 0.6773 (pt0) REVERT: F 71 HIS cc_start: 0.7538 (t-90) cc_final: 0.7252 (t-90) REVERT: H 37 LYS cc_start: 0.7552 (mmmt) cc_final: 0.7215 (tmtm) REVERT: H 118 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7078 (mm) outliers start: 31 outliers final: 10 residues processed: 150 average time/residue: 0.7257 time to fit residues: 116.2572 Evaluate side-chains 144 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090369 restraints weight = 35472.900| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.15 r_work: 0.2906 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11794 Z= 0.105 Angle : 0.443 6.700 15926 Z= 0.234 Chirality : 0.041 0.140 1801 Planarity : 0.003 0.041 2049 Dihedral : 6.289 81.940 1674 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.15 % Allowed : 18.74 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.85 (0.23), residues: 1451 helix: 2.16 (0.19), residues: 799 sheet: 0.48 (0.39), residues: 202 loop : -0.05 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.012 0.002 TYR A 260 PHE 0.007 0.001 PHE H 93 TRP 0.005 0.001 TRP H 108 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00231 (11792) covalent geometry : angle 0.44261 (15926) hydrogen bonds : bond 0.04230 ( 641) hydrogen bonds : angle 4.09859 ( 1871) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: A 145 ARG cc_start: 0.7764 (mtm110) cc_final: 0.6548 (pmt170) REVERT: A 226 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7764 (mptp) REVERT: A 291 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8282 (mtm) REVERT: A 347 LYS cc_start: 0.8233 (mttm) cc_final: 0.7810 (mtmt) REVERT: A 357 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8623 (m) REVERT: A 362 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: A 364 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: A 417 GLU cc_start: 0.7755 (tt0) cc_final: 0.7159 (mp0) REVERT: A 435 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 18 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7576 (mtt90) REVERT: D 89 ARG cc_start: 0.7631 (mmt90) cc_final: 0.6719 (mtp85) REVERT: E 145 ARG cc_start: 0.7452 (mtm110) cc_final: 0.6696 (pmt170) REVERT: E 247 MET cc_start: 0.8830 (mtt) cc_final: 0.8422 (mtt) REVERT: E 273 ARG cc_start: 0.8173 (ttt90) cc_final: 0.7828 (ttt90) REVERT: E 275 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7529 (ttt-90) REVERT: E 417 GLU cc_start: 0.7853 (tt0) cc_final: 0.7124 (mp0) REVERT: F 42 GLU cc_start: 0.7770 (tt0) cc_final: 0.7034 (pt0) REVERT: F 71 HIS cc_start: 0.7800 (t-90) cc_final: 0.7567 (t-90) REVERT: H 118 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7143 (mm) outliers start: 25 outliers final: 11 residues processed: 146 average time/residue: 0.7360 time to fit residues: 114.4078 Evaluate side-chains 144 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.090675 restraints weight = 33591.487| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.09 r_work: 0.2913 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11794 Z= 0.105 Angle : 0.449 8.172 15926 Z= 0.235 Chirality : 0.041 0.140 1801 Planarity : 0.003 0.041 2049 Dihedral : 6.120 82.261 1674 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 19.14 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.84 (0.23), residues: 1451 helix: 2.15 (0.19), residues: 799 sheet: 0.47 (0.39), residues: 202 loop : -0.04 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.012 0.001 TYR E 80 PHE 0.007 0.001 PHE E 408 TRP 0.005 0.001 TRP H 108 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00229 (11792) covalent geometry : angle 0.44923 (15926) hydrogen bonds : bond 0.04154 ( 641) hydrogen bonds : angle 4.09385 ( 1871) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: A 145 ARG cc_start: 0.7778 (mtm110) cc_final: 0.6567 (pmt170) REVERT: A 226 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7766 (mptp) REVERT: A 291 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: A 347 LYS cc_start: 0.8239 (mttm) cc_final: 0.7795 (mtmt) REVERT: A 362 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: A 364 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: A 417 GLU cc_start: 0.7760 (tt0) cc_final: 0.7175 (mp0) REVERT: A 435 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 18 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7588 (mtt90) REVERT: D 89 ARG cc_start: 0.7626 (mmt90) cc_final: 0.6721 (mtp85) REVERT: E 145 ARG cc_start: 0.7465 (mtm110) cc_final: 0.6720 (pmt170) REVERT: E 247 MET cc_start: 0.8831 (mtt) cc_final: 0.8433 (mtt) REVERT: E 273 ARG cc_start: 0.8179 (ttt90) cc_final: 0.7850 (ttt90) REVERT: E 275 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7551 (ttt-90) REVERT: E 417 GLU cc_start: 0.7864 (tt0) cc_final: 0.7136 (mp0) REVERT: F 42 GLU cc_start: 0.7746 (tt0) cc_final: 0.7035 (pt0) REVERT: F 71 HIS cc_start: 0.7769 (t-90) cc_final: 0.7559 (t-90) REVERT: H 118 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7155 (mm) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 0.8080 time to fit residues: 122.8243 Evaluate side-chains 146 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN H 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089950 restraints weight = 43835.480| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.76 r_work: 0.2877 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11794 Z= 0.108 Angle : 0.450 7.750 15926 Z= 0.236 Chirality : 0.041 0.141 1801 Planarity : 0.003 0.040 2049 Dihedral : 5.981 81.570 1674 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.15 % Allowed : 18.82 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.84 (0.23), residues: 1451 helix: 2.16 (0.19), residues: 799 sheet: 0.43 (0.39), residues: 201 loop : -0.03 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.012 0.002 TYR E 80 PHE 0.007 0.001 PHE H 93 TRP 0.008 0.001 TRP I 168 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00240 (11792) covalent geometry : angle 0.45011 (15926) hydrogen bonds : bond 0.04257 ( 641) hydrogen bonds : angle 4.10360 ( 1871) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: A 145 ARG cc_start: 0.7826 (mtm110) cc_final: 0.6557 (pmt170) REVERT: A 226 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7786 (mptp) REVERT: A 291 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8297 (mtm) REVERT: A 347 LYS cc_start: 0.8267 (mttm) cc_final: 0.7812 (mtmt) REVERT: A 362 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: A 364 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: A 417 GLU cc_start: 0.7841 (tt0) cc_final: 0.7201 (mp0) REVERT: A 435 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 18 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7648 (mtt90) REVERT: D 89 ARG cc_start: 0.7624 (mmt90) cc_final: 0.6720 (mtp85) REVERT: I 189 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: E 100 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: E 145 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6744 (pmt170) REVERT: E 247 MET cc_start: 0.8854 (mtt) cc_final: 0.8465 (mtt) REVERT: E 273 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7864 (ttt180) REVERT: E 275 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7525 (tpt-90) REVERT: E 417 GLU cc_start: 0.7921 (tt0) cc_final: 0.7149 (mp0) REVERT: F 42 GLU cc_start: 0.7828 (tt0) cc_final: 0.7106 (pt0) REVERT: F 71 HIS cc_start: 0.7839 (t-90) cc_final: 0.7611 (t-90) REVERT: H 118 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7128 (mm) outliers start: 25 outliers final: 13 residues processed: 146 average time/residue: 0.7908 time to fit residues: 123.1151 Evaluate side-chains 150 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 134 optimal weight: 0.0970 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.086871 restraints weight = 37260.176| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.15 r_work: 0.2853 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11794 Z= 0.169 Angle : 0.520 9.086 15926 Z= 0.273 Chirality : 0.044 0.149 1801 Planarity : 0.004 0.041 2049 Dihedral : 6.613 83.182 1674 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.83 % Allowed : 19.22 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.64 (0.23), residues: 1451 helix: 1.97 (0.19), residues: 799 sheet: 0.48 (0.39), residues: 200 loop : -0.14 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 292 TYR 0.015 0.002 TYR A 260 PHE 0.009 0.002 PHE E 141 TRP 0.006 0.001 TRP H 108 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00406 (11792) covalent geometry : angle 0.51990 (15926) hydrogen bonds : bond 0.05247 ( 641) hydrogen bonds : angle 4.31353 ( 1871) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7369 (mtp-110) REVERT: A 226 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7874 (mtmm) REVERT: A 347 LYS cc_start: 0.8043 (mttm) cc_final: 0.7578 (mtmt) REVERT: A 364 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: A 417 GLU cc_start: 0.7709 (tt0) cc_final: 0.6897 (mp0) REVERT: B 18 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7349 (mtt90) REVERT: D 89 ARG cc_start: 0.7508 (mmt90) cc_final: 0.6540 (mtp85) REVERT: E 145 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6597 (pmt170) REVERT: E 247 MET cc_start: 0.8714 (mtt) cc_final: 0.8320 (mtt) REVERT: E 273 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7641 (ttt180) REVERT: E 275 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7435 (ttt-90) REVERT: E 417 GLU cc_start: 0.7693 (tt0) cc_final: 0.6805 (mp0) REVERT: F 71 HIS cc_start: 0.7621 (t-90) cc_final: 0.7293 (t-90) REVERT: H 118 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7147 (mm) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.7917 time to fit residues: 125.6455 Evaluate side-chains 151 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.086836 restraints weight = 45567.674| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.45 r_work: 0.2844 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11794 Z= 0.149 Angle : 0.501 8.820 15926 Z= 0.263 Chirality : 0.043 0.145 1801 Planarity : 0.004 0.040 2049 Dihedral : 6.528 80.550 1674 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.52 % Allowed : 19.78 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.64 (0.23), residues: 1451 helix: 1.98 (0.19), residues: 799 sheet: 0.45 (0.39), residues: 200 loop : -0.16 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.014 0.002 TYR A 260 PHE 0.008 0.002 PHE E 141 TRP 0.006 0.001 TRP H 108 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00353 (11792) covalent geometry : angle 0.50130 (15926) hydrogen bonds : bond 0.04934 ( 641) hydrogen bonds : angle 4.27142 ( 1871) Misc. bond : bond 0.00057 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7531 (mtp-110) REVERT: A 226 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8037 (mtmm) REVERT: A 347 LYS cc_start: 0.8273 (mttm) cc_final: 0.7835 (mtmt) REVERT: A 364 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: A 417 GLU cc_start: 0.7890 (tt0) cc_final: 0.7214 (mp0) REVERT: B 18 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7643 (mtt90) REVERT: D 89 ARG cc_start: 0.7683 (mmt90) cc_final: 0.6749 (mtp85) REVERT: I 174 VAL cc_start: 0.7524 (p) cc_final: 0.7284 (t) REVERT: E 145 ARG cc_start: 0.7651 (mtm110) cc_final: 0.6891 (pmt170) REVERT: E 247 MET cc_start: 0.8832 (mtt) cc_final: 0.8442 (mtt) REVERT: E 273 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7835 (ttt180) REVERT: E 275 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7573 (tpt-90) REVERT: E 417 GLU cc_start: 0.7900 (tt0) cc_final: 0.7125 (mp0) REVERT: F 71 HIS cc_start: 0.7856 (t-90) cc_final: 0.7598 (t-90) REVERT: H 118 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7197 (mm) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.7570 time to fit residues: 114.8955 Evaluate side-chains 149 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 39 optimal weight: 0.0050 chunk 132 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087681 restraints weight = 42075.500| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.33 r_work: 0.2867 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11794 Z= 0.133 Angle : 0.483 8.702 15926 Z= 0.255 Chirality : 0.043 0.151 1801 Planarity : 0.004 0.041 2049 Dihedral : 6.464 79.935 1674 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.52 % Allowed : 19.86 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.68 (0.23), residues: 1451 helix: 2.02 (0.19), residues: 799 sheet: 0.40 (0.39), residues: 202 loop : -0.12 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.013 0.002 TYR A 260 PHE 0.008 0.001 PHE E 141 TRP 0.006 0.001 TRP H 108 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00309 (11792) covalent geometry : angle 0.48309 (15926) hydrogen bonds : bond 0.04747 ( 641) hydrogen bonds : angle 4.23285 ( 1871) Misc. bond : bond 0.00044 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5372.13 seconds wall clock time: 92 minutes 10.80 seconds (5530.80 seconds total)