Starting phenix.real_space_refine on Wed May 14 08:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rme_19359/05_2025/8rme_19359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rme_19359/05_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_19359/05_2025/8rme_19359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rme_19359/05_2025/8rme_19359.map" model { file = "/net/cci-nas-00/data/ceres_data/8rme_19359/05_2025/8rme_19359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rme_19359/05_2025/8rme_19359.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.91, per 1000 atoms: 0.84 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: 3.07 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.15 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: 3.45 Time building geometry restraints manager: 3.53 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 157 or resid 201)) selection = (chain 'H' and (resid 36 through 157 or resid 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.560 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.360 ------------------------------------------------------------------------------- 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 : 5.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP E 440 HIS 0.017 0.002 HIS B 71 PHE 0.020 0.002 PHE F 40 TYR 0.016 0.002 TYR A 350 ARG 0.004 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.16070 ( 641) hydrogen bonds : angle 5.97382 ( 1871) covalent geometry : bond 0.00641 (11792) covalent geometry : angle 0.85928 (15926) 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 : 1.306 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: 1.5990 time to fit residues: 303.7967 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 : 1.397 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 G 20 GLN G 25 ASN H 157 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096320 restraints weight = 38207.576| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.02 r_work: 0.3151 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11794 Z= 0.152 Angle : 0.531 8.208 15926 Z= 0.283 Chirality : 0.044 0.173 1801 Planarity : 0.004 0.051 2049 Dihedral : 11.250 169.002 1693 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.07 % Allowed : 18.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1451 helix: 1.56 (0.19), residues: 798 sheet: 0.32 (0.38), residues: 203 loop : -0.26 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 108 HIS 0.004 0.001 HIS E 319 PHE 0.010 0.002 PHE H 93 TYR 0.014 0.002 TYR E 80 ARG 0.006 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 641) hydrogen bonds : angle 4.55026 ( 1871) covalent geometry : bond 0.00352 (11792) covalent geometry : angle 0.53150 (15926) Misc. bond : bond 0.00047 ( 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 176 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8259 (mtmm) REVERT: A 347 LYS cc_start: 0.8452 (mttm) cc_final: 0.8117 (mtmt) REVERT: A 417 GLU cc_start: 0.7825 (tt0) cc_final: 0.7492 (mp0) REVERT: B 41 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7861 (ttm170) REVERT: B 71 HIS cc_start: 0.8156 (t-90) cc_final: 0.7877 (t-170) REVERT: D 89 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7124 (mmp80) REVERT: E 91 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.8229 (mtt-85) REVERT: E 144 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8393 (p) REVERT: E 145 ARG cc_start: 0.7517 (mtm110) cc_final: 0.6838 (pmt170) REVERT: E 247 MET cc_start: 0.8967 (mtt) cc_final: 0.8595 (mtt) REVERT: E 275 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7719 (tpt-90) REVERT: E 347 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7577 (mmtt) REVERT: E 417 GLU cc_start: 0.7998 (tt0) cc_final: 0.7462 (mp0) REVERT: F 18 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: F 71 HIS cc_start: 0.7904 (t-90) cc_final: 0.7699 (t-90) REVERT: H 118 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7734 (mm) outliers start: 24 outliers final: 9 residues processed: 165 average time/residue: 1.5581 time to fit residues: 274.5680 Evaluate side-chains 152 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 B residue 41 ARG Chi-restraints excluded: chain I residue 174 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 41 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 E 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090192 restraints weight = 44852.690| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.69 r_work: 0.2894 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1475 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= 0.104 Angle : 0.454 7.779 15926 Z= 0.242 Chirality : 0.041 0.164 1801 Planarity : 0.003 0.046 2049 Dihedral : 8.958 145.634 1677 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.39 % Allowed : 18.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1451 helix: 1.94 (0.19), residues: 797 sheet: 0.47 (0.39), residues: 201 loop : -0.15 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 108 HIS 0.004 0.001 HIS F 71 PHE 0.010 0.001 PHE H 93 TYR 0.011 0.001 TYR E 80 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 641) hydrogen bonds : angle 4.23984 ( 1871) covalent geometry : bond 0.00222 (11792) covalent geometry : angle 0.45440 (15926) 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 169 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7798 (mtm110) cc_final: 0.6528 (pmt170) REVERT: A 226 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8055 (mtmm) REVERT: A 347 LYS cc_start: 0.8315 (mttm) cc_final: 0.7902 (mtmt) REVERT: A 364 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 417 GLU cc_start: 0.7723 (tt0) cc_final: 0.7135 (mp0) REVERT: B 41 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7746 (ttm170) REVERT: B 71 HIS cc_start: 0.8139 (t-90) cc_final: 0.7807 (t-170) REVERT: D 89 ARG cc_start: 0.7671 (mmt90) cc_final: 0.6783 (mtp85) REVERT: I 164 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7630 (mttt) REVERT: E 145 ARG cc_start: 0.7426 (mtm110) cc_final: 0.6606 (pmt170) REVERT: E 247 MET cc_start: 0.8846 (mtt) cc_final: 0.8428 (mtt) REVERT: E 275 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7377 (tpt-90) REVERT: E 347 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7430 (mmtt) REVERT: E 417 GLU cc_start: 0.7894 (tt0) cc_final: 0.7134 (mp0) REVERT: F 71 HIS cc_start: 0.7959 (t-90) cc_final: 0.7687 (t-90) REVERT: H 118 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7236 (mm) outliers start: 28 outliers final: 7 residues processed: 161 average time/residue: 1.5525 time to fit residues: 267.6907 Evaluate side-chains 149 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 21 LYS Chi-restraints excluded: chain B residue 41 ARG 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 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 overall best weight: 1.0540 ------------------------------------------------------------------------------- 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 E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089058 restraints weight = 37426.560| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.21 r_work: 0.2887 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 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 = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11794 Z= 0.116 Angle : 0.463 7.161 15926 Z= 0.245 Chirality : 0.042 0.142 1801 Planarity : 0.003 0.044 2049 Dihedral : 8.210 126.065 1674 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.31 % Allowed : 17.94 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1451 helix: 2.01 (0.19), residues: 799 sheet: 0.49 (0.39), residues: 200 loop : -0.10 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 108 HIS 0.004 0.001 HIS F 71 PHE 0.008 0.001 PHE H 93 TYR 0.013 0.002 TYR A 260 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 641) hydrogen bonds : angle 4.21569 ( 1871) covalent geometry : bond 0.00260 (11792) covalent geometry : angle 0.46306 (15926) Misc. bond : bond 0.00040 ( 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 167 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: A 145 ARG cc_start: 0.7802 (mtm110) cc_final: 0.6577 (pmt170) REVERT: A 226 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7803 (mptp) REVERT: A 347 LYS cc_start: 0.8307 (mttm) cc_final: 0.7892 (mtmt) REVERT: A 362 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: A 364 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 417 GLU cc_start: 0.7729 (tt0) cc_final: 0.7166 (mp0) REVERT: B 18 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7669 (mtt90) REVERT: B 41 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7782 (ttm170) REVERT: D 89 ARG cc_start: 0.7668 (mmt90) cc_final: 0.6782 (mtp85) REVERT: E 145 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6665 (pmt170) REVERT: E 247 MET cc_start: 0.8871 (mtt) cc_final: 0.8463 (mtt) REVERT: E 275 ARG cc_start: 0.7971 (tpp-160) cc_final: 0.7475 (ttt-90) REVERT: E 347 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7434 (mmtt) REVERT: E 417 GLU cc_start: 0.7877 (tt0) cc_final: 0.7144 (mp0) REVERT: F 71 HIS cc_start: 0.7941 (t-90) cc_final: 0.7693 (t-90) REVERT: H 118 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7204 (mm) outliers start: 27 outliers final: 6 residues processed: 157 average time/residue: 1.5856 time to fit residues: 265.8286 Evaluate side-chains 143 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 362 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 41 ARG 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 90 optimal weight: 3.9990 chunk 131 optimal weight: 0.0020 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.149378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.086634 restraints weight = 41752.256| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.33 r_work: 0.2829 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11794 Z= 0.156 Angle : 0.505 7.307 15926 Z= 0.267 Chirality : 0.044 0.149 1801 Planarity : 0.004 0.043 2049 Dihedral : 7.975 116.717 1674 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.47 % Allowed : 17.78 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1451 helix: 1.93 (0.19), residues: 798 sheet: 0.43 (0.39), residues: 202 loop : -0.20 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 108 HIS 0.008 0.001 HIS B 71 PHE 0.009 0.002 PHE E 141 TYR 0.015 0.002 TYR E 80 ARG 0.004 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 641) hydrogen bonds : angle 4.33386 ( 1871) covalent geometry : bond 0.00371 (11792) covalent geometry : angle 0.50464 (15926) Misc. bond : bond 0.00058 ( 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 168 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: A 145 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7535 (mtp-110) REVERT: A 226 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8039 (mtmm) REVERT: A 347 LYS cc_start: 0.8224 (mttm) cc_final: 0.7786 (mtmt) REVERT: A 417 GLU cc_start: 0.7843 (tt0) cc_final: 0.7168 (mp0) REVERT: B 18 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7587 (mtt90) REVERT: B 41 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8268 (mtt90) REVERT: D 89 ARG cc_start: 0.7666 (mmt90) cc_final: 0.6731 (mtp85) REVERT: E 145 ARG cc_start: 0.7509 (mtm110) cc_final: 0.6710 (pmt170) REVERT: E 247 MET cc_start: 0.8819 (mtt) cc_final: 0.8435 (mtt) REVERT: E 275 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7585 (ttt-90) REVERT: E 417 GLU cc_start: 0.7890 (tt0) cc_final: 0.7034 (mp0) REVERT: F 71 HIS cc_start: 0.7899 (t-90) cc_final: 0.7616 (t-90) REVERT: H 118 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7249 (mm) outliers start: 29 outliers final: 13 residues processed: 157 average time/residue: 1.5676 time to fit residues: 262.9086 Evaluate side-chains 154 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 357 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 37 SER 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 H residue 79 VAL Chi-restraints excluded: chain H residue 86 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 126 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.153155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095650 restraints weight = 36458.439| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.93 r_work: 0.3125 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11794 Z= 0.175 Angle : 0.524 7.767 15926 Z= 0.277 Chirality : 0.044 0.149 1801 Planarity : 0.004 0.043 2049 Dihedral : 7.467 87.331 1674 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 18.34 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1451 helix: 1.86 (0.19), residues: 800 sheet: 0.37 (0.39), residues: 202 loop : -0.23 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 108 HIS 0.007 0.001 HIS B 71 PHE 0.009 0.002 PHE E 141 TYR 0.015 0.002 TYR A 260 ARG 0.003 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 641) hydrogen bonds : angle 4.37752 ( 1871) covalent geometry : bond 0.00422 (11792) covalent geometry : angle 0.52441 (15926) Misc. bond : bond 0.00048 ( 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 164 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7813 (mtp-110) REVERT: A 226 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8324 (mtmm) REVERT: A 347 LYS cc_start: 0.8443 (mttm) cc_final: 0.8063 (mtmt) REVERT: A 362 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: A 364 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7961 (tt0) REVERT: A 417 GLU cc_start: 0.8255 (tt0) cc_final: 0.7634 (mp0) REVERT: B 18 ARG cc_start: 0.8359 (mtt90) cc_final: 0.8090 (mtt90) REVERT: B 41 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8529 (mtt90) REVERT: B 51 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: D 89 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7186 (mtp85) REVERT: E 145 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7021 (pmt170) REVERT: E 247 MET cc_start: 0.8975 (mtt) cc_final: 0.8668 (mtt) REVERT: E 275 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.7959 (ttt-90) REVERT: E 417 GLU cc_start: 0.8252 (tt0) cc_final: 0.7486 (mp0) REVERT: F 71 HIS cc_start: 0.8313 (t-90) cc_final: 0.8063 (t-90) REVERT: H 118 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7380 (mm) outliers start: 26 outliers final: 11 residues processed: 155 average time/residue: 1.5400 time to fit residues: 255.3220 Evaluate side-chains 155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain I residue 151 ASN 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 F residue 23 PHE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 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 101 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.153723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096233 restraints weight = 38069.405| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.97 r_work: 0.3121 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11794 Z= 0.155 Angle : 0.501 7.681 15926 Z= 0.265 Chirality : 0.043 0.146 1801 Planarity : 0.004 0.043 2049 Dihedral : 6.942 76.051 1673 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.23 % Allowed : 18.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1451 helix: 1.91 (0.19), residues: 799 sheet: 0.35 (0.39), residues: 202 loop : -0.26 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 108 HIS 0.006 0.001 HIS B 71 PHE 0.009 0.002 PHE E 141 TYR 0.014 0.002 TYR A 260 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 641) hydrogen bonds : angle 4.31805 ( 1871) covalent geometry : bond 0.00368 (11792) covalent geometry : angle 0.50064 (15926) Misc. bond : bond 0.00050 ( 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 167 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: A 226 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8263 (mtmm) REVERT: A 347 LYS cc_start: 0.8355 (mttm) cc_final: 0.7992 (mtmt) REVERT: A 362 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: A 364 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 417 GLU cc_start: 0.7990 (tt0) cc_final: 0.7526 (mp0) REVERT: B 18 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7934 (mtt90) REVERT: B 41 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8479 (mtt90) REVERT: B 51 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: D 89 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7062 (mtp85) REVERT: E 100 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 145 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7085 (pmt170) REVERT: E 275 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7956 (ttt-90) REVERT: E 417 GLU cc_start: 0.8045 (tt0) cc_final: 0.7378 (mp0) REVERT: H 118 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7417 (mm) outliers start: 26 outliers final: 13 residues processed: 157 average time/residue: 1.5402 time to fit residues: 258.4253 Evaluate side-chains 155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 357 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 51 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 40 VAL Chi-restraints excluded: chain H residue 41 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 E 429 HIS F 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099042 restraints weight = 42229.920| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.09 r_work: 0.3180 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1879 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= 0.101 Angle : 0.448 7.088 15926 Z= 0.237 Chirality : 0.041 0.140 1801 Planarity : 0.003 0.042 2049 Dihedral : 6.479 85.315 1673 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 18.82 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1451 helix: 2.08 (0.19), residues: 798 sheet: 0.42 (0.39), residues: 202 loop : -0.14 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 108 HIS 0.010 0.001 HIS B 71 PHE 0.009 0.001 PHE H 93 TYR 0.012 0.001 TYR E 80 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 641) hydrogen bonds : angle 4.14475 ( 1871) covalent geometry : bond 0.00215 (11792) covalent geometry : angle 0.44785 (15926) Misc. bond : bond 0.00015 ( 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 160 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: A 145 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.6656 (pmt170) REVERT: A 226 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8020 (mptp) REVERT: A 347 LYS cc_start: 0.8432 (mttm) cc_final: 0.8089 (mtmt) REVERT: A 364 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 417 GLU cc_start: 0.7924 (tt0) cc_final: 0.7491 (mp0) REVERT: B 18 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7965 (mtt90) REVERT: D 89 ARG cc_start: 0.7909 (mmt90) cc_final: 0.7073 (mtp85) REVERT: E 100 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: E 145 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7037 (pmt170) REVERT: E 417 GLU cc_start: 0.7995 (tt0) cc_final: 0.7427 (mp0) REVERT: F 42 GLU cc_start: 0.8011 (tt0) cc_final: 0.7399 (pt0) REVERT: H 118 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7336 (mm) outliers start: 21 outliers final: 9 residues processed: 151 average time/residue: 1.6722 time to fit residues: 269.5304 Evaluate side-chains 148 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 357 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain C residue 37 SER 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 41 ASP 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 39 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096937 restraints weight = 40183.040| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.03 r_work: 0.3142 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11794 Z= 0.135 Angle : 0.485 8.918 15926 Z= 0.257 Chirality : 0.042 0.143 1801 Planarity : 0.004 0.042 2049 Dihedral : 6.646 88.257 1673 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.67 % Allowed : 18.90 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1451 helix: 2.03 (0.19), residues: 798 sheet: 0.38 (0.39), residues: 201 loop : -0.15 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 168 HIS 0.011 0.001 HIS F 71 PHE 0.008 0.001 PHE H 93 TYR 0.014 0.002 TYR A 260 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 641) hydrogen bonds : angle 4.24978 ( 1871) covalent geometry : bond 0.00313 (11792) covalent geometry : angle 0.48463 (15926) Misc. bond : bond 0.00045 ( 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 155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: A 145 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.6678 (pmt170) REVERT: A 226 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8046 (mptp) REVERT: A 347 LYS cc_start: 0.8407 (mttm) cc_final: 0.8049 (mtmt) REVERT: A 364 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 417 GLU cc_start: 0.7972 (tt0) cc_final: 0.7522 (mp0) REVERT: B 18 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7939 (mtt90) REVERT: D 89 ARG cc_start: 0.7911 (mmt90) cc_final: 0.7081 (mtp85) REVERT: E 100 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: E 145 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7070 (pmt170) REVERT: E 417 GLU cc_start: 0.7968 (tt0) cc_final: 0.7380 (mp0) REVERT: F 42 GLU cc_start: 0.8029 (tt0) cc_final: 0.7374 (pt0) REVERT: H 118 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7383 (mm) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 1.5569 time to fit residues: 241.5436 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 : 1.373 ------------------------------------------------------------------------------- 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 357 SER 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 100 GLU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain H residue 41 ASP 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 8 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 109 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 F 71 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098743 restraints weight = 46861.704| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.21 r_work: 0.3168 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11794 Z= 0.104 Angle : 0.450 8.743 15926 Z= 0.239 Chirality : 0.041 0.162 1801 Planarity : 0.003 0.041 2049 Dihedral : 6.132 83.338 1673 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.28 % Allowed : 19.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1451 helix: 2.11 (0.19), residues: 799 sheet: 0.41 (0.39), residues: 202 loop : -0.09 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 168 HIS 0.005 0.001 HIS F 71 PHE 0.008 0.001 PHE D 93 TYR 0.012 0.001 TYR A 260 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 641) hydrogen bonds : angle 4.13376 ( 1871) covalent geometry : bond 0.00226 (11792) covalent geometry : angle 0.45046 (15926) Misc. bond : bond 0.00025 ( 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 151 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: A 145 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.6648 (pmt170) REVERT: A 226 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8024 (mptp) REVERT: A 347 LYS cc_start: 0.8425 (mttm) cc_final: 0.8076 (mtmt) REVERT: A 364 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 417 GLU cc_start: 0.7942 (tt0) cc_final: 0.7500 (mp0) REVERT: B 18 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7961 (mtt90) REVERT: D 89 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7066 (mtp85) REVERT: E 100 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: E 145 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7064 (pmt170) REVERT: E 273 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7807 (ttt180) REVERT: E 417 GLU cc_start: 0.7996 (tt0) cc_final: 0.7448 (mp0) REVERT: F 42 GLU cc_start: 0.8030 (tt0) cc_final: 0.7354 (pt0) REVERT: H 118 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7280 (mm) outliers start: 14 outliers final: 9 residues processed: 144 average time/residue: 1.6036 time to fit residues: 246.7511 Evaluate side-chains 148 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 357 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain C residue 37 SER 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 41 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094691 restraints weight = 38887.760| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.99 r_work: 0.3110 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11794 Z= 0.214 Angle : 0.567 8.876 15926 Z= 0.299 Chirality : 0.046 0.156 1801 Planarity : 0.004 0.043 2049 Dihedral : 6.913 89.413 1673 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 19.06 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1451 helix: 1.83 (0.18), residues: 798 sheet: 0.30 (0.38), residues: 202 loop : -0.26 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 168 HIS 0.007 0.001 HIS F 71 PHE 0.010 0.002 PHE E 141 TYR 0.017 0.003 TYR E 80 ARG 0.004 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.05792 ( 641) hydrogen bonds : angle 4.44985 ( 1871) covalent geometry : bond 0.00525 (11792) covalent geometry : angle 0.56701 (15926) Misc. bond : bond 0.00080 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10730.86 seconds wall clock time: 185 minutes 22.37 seconds (11122.37 seconds total)