Starting phenix.real_space_refine on Wed May 28 03:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dli_46979/05_2025/9dli_46979.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dli_46979/05_2025/9dli_46979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dli_46979/05_2025/9dli_46979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dli_46979/05_2025/9dli_46979.map" model { file = "/net/cci-nas-00/data/ceres_data/9dli_46979/05_2025/9dli_46979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dli_46979/05_2025/9dli_46979.cif" } resolution = 2.7 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= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 10060 2.51 5 N 2392 2.21 5 O 2704 1.98 5 H 15064 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30300 Number of models: 1 Model: "" Number of chains: 4 Chain: "A1" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7575 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 2 Chain: "A2" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7575 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 2 Chain: "A3" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7575 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 2 Chain: "A4" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7575 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 2 Time building chain proxies: 20.38, per 1000 atoms: 0.67 Number of scatterers: 30300 At special positions: 0 Unit cell: (113.548, 113.872, 100.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2704 8.00 N 2392 7.00 C 10060 6.00 H 15064 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYSA1 152 " - pdb=" SG CYSA1 165 " distance=2.03 Simple disulfide: pdb=" SG CYSA2 152 " - pdb=" SG CYSA2 165 " distance=2.03 Simple disulfide: pdb=" SG CYSA3 152 " - pdb=" SG CYSA3 165 " distance=2.03 Simple disulfide: pdb=" SG CYSA4 152 " - pdb=" SG CYSA4 165 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 12 sheets defined 61.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A1' and resid 34 through 61 removed outlier: 3.716A pdb=" N SERA1 40 " --> pdb=" O LYSA1 36 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARGA1 43 " --> pdb=" O LYSA1 39 " (cutoff:3.500A) Processing helix chain 'A1' and resid 62 through 64 No H-bonds generated for 'chain 'A1' and resid 62 through 64' Processing helix chain 'A1' and resid 65 through 79 removed outlier: 3.909A pdb=" N TYRA1 69 " --> pdb=" O SERA1 65 " (cutoff:3.500A) Processing helix chain 'A1' and resid 90 through 94 Processing helix chain 'A1' and resid 96 through 106 Processing helix chain 'A1' and resid 106 through 113 Processing helix chain 'A1' and resid 155 through 159 removed outlier: 3.711A pdb=" N ARGA1 159 " --> pdb=" O GLNA1 156 " (cutoff:3.500A) Processing helix chain 'A1' and resid 219 through 233 Processing helix chain 'A1' and resid 288 through 314 Processing helix chain 'A1' and resid 326 through 353 removed outlier: 3.521A pdb=" N SERA1 351 " --> pdb=" O ILEA1 347 " (cutoff:3.500A) Processing helix chain 'A1' and resid 353 through 360 removed outlier: 3.910A pdb=" N LEUA1 357 " --> pdb=" O VALA1 353 " (cutoff:3.500A) Processing helix chain 'A1' and resid 369 through 393 Processing helix chain 'A1' and resid 394 through 397 Processing helix chain 'A1' and resid 403 through 441 removed outlier: 4.730A pdb=" N LYSA1 416 " --> pdb=" O SERA1 412 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASPA1 417 " --> pdb=" O ARGA1 413 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILEA1 428 " --> pdb=" O META1 424 " (cutoff:3.500A) Processing helix chain 'A1' and resid 444 through 448 Processing helix chain 'A1' and resid 449 through 463 Processing helix chain 'A1' and resid 466 through 474 removed outlier: 3.649A pdb=" N ASNA1 474 " --> pdb=" O ILEA1 470 " (cutoff:3.500A) Processing helix chain 'A1' and resid 476 through 490 removed outlier: 3.881A pdb=" N ILEA1 480 " --> pdb=" O VALA1 476 " (cutoff:3.500A) Processing helix chain 'A1' and resid 493 through 513 removed outlier: 4.224A pdb=" N PHEA1 497 " --> pdb=" O LEUA1 493 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEUA1 498 " --> pdb=" O LEUA1 494 " (cutoff:3.500A) Processing helix chain 'A2' and resid 35 through 62 removed outlier: 3.878A pdb=" N SERA2 40 " --> pdb=" O LYSA2 36 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGA2 43 " --> pdb=" O LYSA2 39 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N META2 62 " --> pdb=" O LEUA2 58 " (cutoff:3.500A) Processing helix chain 'A2' and resid 65 through 79 removed outlier: 3.876A pdb=" N TYRA2 69 " --> pdb=" O SERA2 65 " (cutoff:3.500A) Processing helix chain 'A2' and resid 90 through 94 Processing helix chain 'A2' and resid 96 through 106 Processing helix chain 'A2' and resid 106 through 113 Processing helix chain 'A2' and resid 219 through 233 Processing helix chain 'A2' and resid 288 through 314 removed outlier: 3.903A pdb=" N CYSA2 302 " --> pdb=" O GLUA2 298 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHEA2 303 " --> pdb=" O ILEA2 299 " (cutoff:3.500A) Processing helix chain 'A2' and resid 326 through 353 removed outlier: 3.645A pdb=" N SERA2 351 " --> pdb=" O ILEA2 347 " (cutoff:3.500A) Processing helix chain 'A2' and resid 353 through 360 removed outlier: 3.670A pdb=" N LEUA2 357 " --> pdb=" O VALA2 353 " (cutoff:3.500A) Processing helix chain 'A2' and resid 369 through 393 Processing helix chain 'A2' and resid 394 through 397 Processing helix chain 'A2' and resid 401 through 441 removed outlier: 3.581A pdb=" N GLNA2 406 " --> pdb=" O ARGA2 402 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYSA2 416 " --> pdb=" O SERA2 412 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASPA2 417 " --> pdb=" O ARGA2 413 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILEA2 428 " --> pdb=" O META2 424 " (cutoff:3.500A) Processing helix chain 'A2' and resid 444 through 448 Processing helix chain 'A2' and resid 449 through 463 Processing helix chain 'A2' and resid 466 through 474 removed outlier: 3.568A pdb=" N ILEA2 470 " --> pdb=" O ASNA2 466 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASNA2 474 " --> pdb=" O ILEA2 470 " (cutoff:3.500A) Processing helix chain 'A2' and resid 476 through 490 removed outlier: 3.781A pdb=" N ILEA2 480 " --> pdb=" O VALA2 476 " (cutoff:3.500A) Processing helix chain 'A2' and resid 493 through 513 removed outlier: 4.264A pdb=" N PHEA2 497 " --> pdb=" O LEUA2 493 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEUA2 498 " --> pdb=" O LEUA2 494 " (cutoff:3.500A) Processing helix chain 'A3' and resid 35 through 61 removed outlier: 3.642A pdb=" N SERA3 40 " --> pdb=" O LYSA3 36 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARGA3 43 " --> pdb=" O LYSA3 39 " (cutoff:3.500A) Processing helix chain 'A3' and resid 62 through 64 No H-bonds generated for 'chain 'A3' and resid 62 through 64' Processing helix chain 'A3' and resid 65 through 79 removed outlier: 4.035A pdb=" N TYRA3 69 " --> pdb=" O SERA3 65 " (cutoff:3.500A) Processing helix chain 'A3' and resid 90 through 94 removed outlier: 3.522A pdb=" N LEUA3 94 " --> pdb=" O PHEA3 91 " (cutoff:3.500A) Processing helix chain 'A3' and resid 96 through 106 Processing helix chain 'A3' and resid 106 through 113 Processing helix chain 'A3' and resid 219 through 233 Processing helix chain 'A3' and resid 288 through 314 removed outlier: 3.731A pdb=" N CYSA3 302 " --> pdb=" O GLUA3 298 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHEA3 303 " --> pdb=" O ILEA3 299 " (cutoff:3.500A) Processing helix chain 'A3' and resid 326 through 353 removed outlier: 3.648A pdb=" N THRA3 350 " --> pdb=" O ASNA3 346 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SERA3 351 " --> pdb=" O ILEA3 347 " (cutoff:3.500A) Processing helix chain 'A3' and resid 353 through 360 removed outlier: 3.666A pdb=" N LEUA3 357 " --> pdb=" O VALA3 353 " (cutoff:3.500A) Processing helix chain 'A3' and resid 369 through 393 Processing helix chain 'A3' and resid 394 through 397 Processing helix chain 'A3' and resid 403 through 441 removed outlier: 4.714A pdb=" N LYSA3 416 " --> pdb=" O SERA3 412 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASPA3 417 " --> pdb=" O ARGA3 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILEA3 428 " --> pdb=" O META3 424 " (cutoff:3.500A) Processing helix chain 'A3' and resid 444 through 448 Processing helix chain 'A3' and resid 449 through 463 Processing helix chain 'A3' and resid 466 through 474 removed outlier: 3.537A pdb=" N ILEA3 470 " --> pdb=" O ASNA3 466 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASNA3 474 " --> pdb=" O ILEA3 470 " (cutoff:3.500A) Processing helix chain 'A3' and resid 476 through 491 removed outlier: 3.862A pdb=" N ILEA3 480 " --> pdb=" O VALA3 476 " (cutoff:3.500A) Processing helix chain 'A3' and resid 493 through 513 removed outlier: 4.274A pdb=" N PHEA3 497 " --> pdb=" O LEUA3 493 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEUA3 498 " --> pdb=" O LEUA3 494 " (cutoff:3.500A) Processing helix chain 'A4' and resid 35 through 61 Processing helix chain 'A4' and resid 62 through 64 No H-bonds generated for 'chain 'A4' and resid 62 through 64' Processing helix chain 'A4' and resid 65 through 79 removed outlier: 3.958A pdb=" N TYRA4 69 " --> pdb=" O SERA4 65 " (cutoff:3.500A) Processing helix chain 'A4' and resid 90 through 94 Processing helix chain 'A4' and resid 96 through 106 Processing helix chain 'A4' and resid 106 through 113 Processing helix chain 'A4' and resid 155 through 159 removed outlier: 3.653A pdb=" N ARGA4 159 " --> pdb=" O GLNA4 156 " (cutoff:3.500A) Processing helix chain 'A4' and resid 219 through 233 Processing helix chain 'A4' and resid 288 through 314 removed outlier: 3.617A pdb=" N CYSA4 302 " --> pdb=" O GLUA4 298 " (cutoff:3.500A) Processing helix chain 'A4' and resid 326 through 353 removed outlier: 3.643A pdb=" N THRA4 350 " --> pdb=" O ASNA4 346 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SERA4 351 " --> pdb=" O ILEA4 347 " (cutoff:3.500A) Processing helix chain 'A4' and resid 353 through 360 removed outlier: 3.863A pdb=" N LEUA4 357 " --> pdb=" O VALA4 353 " (cutoff:3.500A) Processing helix chain 'A4' and resid 369 through 393 Processing helix chain 'A4' and resid 394 through 397 Processing helix chain 'A4' and resid 403 through 441 removed outlier: 4.622A pdb=" N LYSA4 416 " --> pdb=" O SERA4 412 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASPA4 417 " --> pdb=" O ARGA4 413 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILEA4 428 " --> pdb=" O META4 424 " (cutoff:3.500A) Processing helix chain 'A4' and resid 444 through 448 Processing helix chain 'A4' and resid 449 through 463 Processing helix chain 'A4' and resid 466 through 474 removed outlier: 3.538A pdb=" N ILEA4 470 " --> pdb=" O ASNA4 466 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASNA4 474 " --> pdb=" O ILEA4 470 " (cutoff:3.500A) Processing helix chain 'A4' and resid 476 through 491 removed outlier: 3.884A pdb=" N ILEA4 480 " --> pdb=" O VALA4 476 " (cutoff:3.500A) Processing helix chain 'A4' and resid 493 through 513 removed outlier: 4.237A pdb=" N PHEA4 497 " --> pdb=" O LEUA4 493 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEUA4 498 " --> pdb=" O LEUA4 494 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A1' and resid 134 through 136 removed outlier: 6.644A pdb=" N LEUA1 145 " --> pdb=" O ARGA1 241 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THRA1 243 " --> pdb=" O ARGA1 143 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARGA1 143 " --> pdb=" O THRA1 243 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILEA1 245 " --> pdb=" O ARGA1 141 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARGA1 141 " --> pdb=" O ILEA1 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A1' and resid 134 through 136 Processing sheet with id=AA3, first strand: chain 'A1' and resid 200 through 201 Processing sheet with id=AA4, first strand: chain 'A2' and resid 134 through 136 removed outlier: 6.676A pdb=" N LEUA2 145 " --> pdb=" O ARGA2 241 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THRA2 243 " --> pdb=" O ARGA2 143 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARGA2 143 " --> pdb=" O THRA2 243 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILEA2 245 " --> pdb=" O ARGA2 141 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARGA2 141 " --> pdb=" O ILEA2 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A2' and resid 134 through 136 Processing sheet with id=AA6, first strand: chain 'A2' and resid 200 through 201 Processing sheet with id=AA7, first strand: chain 'A3' and resid 134 through 136 removed outlier: 6.677A pdb=" N LEUA3 145 " --> pdb=" O ARGA3 241 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THRA3 243 " --> pdb=" O ARGA3 143 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARGA3 143 " --> pdb=" O THRA3 243 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILEA3 245 " --> pdb=" O ARGA3 141 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARGA3 141 " --> pdb=" O ILEA3 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A3' and resid 134 through 136 Processing sheet with id=AA9, first strand: chain 'A3' and resid 200 through 201 Processing sheet with id=AB1, first strand: chain 'A4' and resid 134 through 136 removed outlier: 6.645A pdb=" N LEUA4 145 " --> pdb=" O ARGA4 241 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THRA4 243 " --> pdb=" O ARGA4 143 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARGA4 143 " --> pdb=" O THRA4 243 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILEA4 245 " --> pdb=" O ARGA4 141 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARGA4 141 " --> pdb=" O ILEA4 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A4' and resid 134 through 136 Processing sheet with id=AB3, first strand: chain 'A4' and resid 200 through 201 921 hydrogen bonds defined for protein. 2652 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: 13.11 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.07: 3152 1.07 - 1.25: 14198 1.25 - 1.44: 4774 1.44 - 1.63: 8452 1.63 - 1.82: 120 Bond restraints: 30696 Sorted by residual: bond pdb=" CD2 PHEA3 491 " pdb=" HD2 PHEA3 491 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SERA3 95 " pdb=" H SERA3 95 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N PHEA3 369 " pdb=" H PHEA3 369 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLUA1 174 " pdb=" H GLUA1 174 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASNA4 364 " pdb="HD21 ASNA4 364 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 30691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 47567 2.60 - 5.21: 5751 5.21 - 7.81: 1714 7.81 - 10.41: 64 10.41 - 13.02: 32 Bond angle restraints: 55128 Sorted by residual: angle pdb=" CA PHEA1 491 " pdb=" CB PHEA1 491 " pdb=" CG PHEA1 491 " ideal model delta sigma weight residual 113.80 120.76 -6.96 1.00e+00 1.00e+00 4.85e+01 angle pdb=" CA PHEA4 491 " pdb=" CB PHEA4 491 " pdb=" CG PHEA4 491 " ideal model delta sigma weight residual 113.80 120.45 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" CA PHEA3 491 " pdb=" CB PHEA3 491 " pdb=" CG PHEA3 491 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA PHEA2 491 " pdb=" CB PHEA2 491 " pdb=" CG PHEA2 491 " ideal model delta sigma weight residual 113.80 120.05 -6.25 1.00e+00 1.00e+00 3.91e+01 angle pdb=" N PHEA4 131 " pdb=" CA PHEA4 131 " pdb=" C PHEA4 131 " ideal model delta sigma weight residual 109.24 101.16 8.08 1.51e+00 4.39e-01 2.86e+01 ... (remaining 55123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 13366 16.98 - 33.97: 716 33.97 - 50.95: 185 50.95 - 67.94: 252 67.94 - 84.92: 29 Dihedral angle restraints: 14548 sinusoidal: 7488 harmonic: 7060 Sorted by residual: dihedral pdb=" CB CYSA4 152 " pdb=" SG CYSA4 152 " pdb=" SG CYSA4 165 " pdb=" CB CYSA4 165 " ideal model delta sinusoidal sigma weight residual 93.00 145.12 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYSA3 152 " pdb=" SG CYSA3 152 " pdb=" SG CYSA3 165 " pdb=" CB CYSA3 165 " ideal model delta sinusoidal sigma weight residual 93.00 144.55 -51.55 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CA ILEA2 130 " pdb=" C ILEA2 130 " pdb=" N PHEA2 131 " pdb=" CA PHEA2 131 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 14545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1333 0.068 - 0.135: 804 0.135 - 0.203: 193 0.203 - 0.270: 40 0.270 - 0.338: 6 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA PHEA1 426 " pdb=" N PHEA1 426 " pdb=" C PHEA1 426 " pdb=" CB PHEA1 426 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA PHEA4 426 " pdb=" N PHEA4 426 " pdb=" C PHEA4 426 " pdb=" CB PHEA4 426 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA PHEA3 426 " pdb=" N PHEA3 426 " pdb=" C PHEA3 426 " pdb=" CB PHEA3 426 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2373 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGA1 261 " -0.430 9.50e-02 1.11e+02 2.13e-01 5.74e+02 pdb=" NE ARGA1 261 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARGA1 261 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARGA1 261 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARGA1 261 " 0.127 2.00e-02 2.50e+03 pdb="HH11 ARGA1 261 " -0.124 2.00e-02 2.50e+03 pdb="HH12 ARGA1 261 " 0.255 2.00e-02 2.50e+03 pdb="HH21 ARGA1 261 " -0.336 2.00e-02 2.50e+03 pdb="HH22 ARGA1 261 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGA2 261 " -0.401 9.50e-02 1.11e+02 2.01e-01 5.28e+02 pdb=" NE ARGA2 261 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARGA2 261 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARGA2 261 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARGA2 261 " 0.131 2.00e-02 2.50e+03 pdb="HH11 ARGA2 261 " -0.110 2.00e-02 2.50e+03 pdb="HH12 ARGA2 261 " 0.237 2.00e-02 2.50e+03 pdb="HH21 ARGA2 261 " -0.327 2.00e-02 2.50e+03 pdb="HH22 ARGA2 261 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPA1 328 " 0.165 2.00e-02 2.50e+03 6.98e-02 1.95e+02 pdb=" CG TRPA1 328 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRPA1 328 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRPA1 328 " -0.042 2.00e-02 2.50e+03 pdb=" NE1 TRPA1 328 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TRPA1 328 " -0.040 2.00e-02 2.50e+03 pdb=" CE3 TRPA1 328 " -0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRPA1 328 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRPA1 328 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRPA1 328 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TRPA1 328 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRPA1 328 " -0.073 2.00e-02 2.50e+03 pdb=" HE3 TRPA1 328 " -0.098 2.00e-02 2.50e+03 pdb=" HZ2 TRPA1 328 " 0.036 2.00e-02 2.50e+03 pdb=" HZ3 TRPA1 328 " -0.022 2.00e-02 2.50e+03 pdb=" HH2 TRPA1 328 " 0.129 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1557 2.18 - 2.79: 53466 2.79 - 3.39: 85335 3.39 - 4.00: 116686 4.00 - 4.60: 167283 Nonbonded interactions: 424327 Sorted by model distance: nonbonded pdb=" HH TYRA4 169 " pdb=" OE2 GLUA4 174 " model vdw 1.578 2.450 nonbonded pdb=" HH TYRA2 169 " pdb=" OE2 GLUA2 174 " model vdw 1.579 2.450 nonbonded pdb=" HH TYRA3 169 " pdb=" OE2 GLUA3 174 " model vdw 1.581 2.450 nonbonded pdb=" HG SERA3 448 " pdb=" OE1 GLUA3 452 " model vdw 1.583 2.450 nonbonded pdb=" HG1 THRA2 449 " pdb=" OE1 GLUA2 452 " model vdw 1.587 2.450 ... (remaining 424322 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 94.840 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 65.350 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.110 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:17.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 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 : 0.013 0.041 15636 Z= 0.711 Angle : 1.663 8.082 21216 Z= 1.129 Chirality : 0.085 0.338 2376 Planarity : 0.014 0.130 2636 Dihedral : 13.116 84.919 5488 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.36 % Allowed : 3.53 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.18), residues: 1824 helix: -0.12 (0.14), residues: 1024 sheet: 0.95 (0.38), residues: 160 loop : -0.75 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.022 TRPA4 276 HIS 0.008 0.004 HISA4 371 PHE 0.084 0.012 PHEA2 421 TYR 0.151 0.022 TYRA3 68 ARG 0.012 0.002 ARGA3 146 Details of bonding type rmsd hydrogen bonds : bond 0.16282 ( 913) hydrogen bonds : angle 6.50064 ( 2652) SS BOND : bond 0.00195 ( 4) SS BOND : angle 1.80530 ( 8) covalent geometry : bond 0.01262 (15632) covalent geometry : angle 1.66325 (21208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 329 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 9 residues processed: 335 average time/residue: 2.1067 time to fit residues: 802.0743 Evaluate side-chains 203 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 249 VAL Chi-restraints excluded: chain A1 residue 461 ILE Chi-restraints excluded: chain A2 residue 213 TYR Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 461 ILE Chi-restraints excluded: chain A4 residue 343 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 457 GLN A1 495 ASN A1 502 ASN A2 457 GLN A2 495 ASN A3 399 ASN A3 457 GLN A4 457 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.202498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170513 restraints weight = 44070.828| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.82 r_work: 0.3876 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15636 Z= 0.150 Angle : 0.568 5.757 21216 Z= 0.323 Chirality : 0.040 0.153 2376 Planarity : 0.004 0.037 2636 Dihedral : 5.791 33.394 2037 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.73 % Allowed : 11.42 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.90 (0.19), residues: 1824 helix: 1.33 (0.15), residues: 1040 sheet: 0.20 (0.37), residues: 184 loop : -0.48 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPA4 235 HIS 0.003 0.001 HISA4 200 PHE 0.027 0.002 PHEA2 421 TYR 0.024 0.002 TYRA3 68 ARG 0.003 0.000 ARGA4 143 Details of bonding type rmsd hydrogen bonds : bond 0.05357 ( 913) hydrogen bonds : angle 4.60140 ( 2652) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.51641 ( 8) covalent geometry : bond 0.00308 (15632) covalent geometry : angle 0.56808 (21208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 330 CYS cc_start: 0.7782 (t) cc_final: 0.7366 (p) REVERT: A2 330 CYS cc_start: 0.7836 (t) cc_final: 0.7561 (p) REVERT: A2 386 THR cc_start: 0.6931 (p) cc_final: 0.6724 (m) REVERT: A2 442 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8245 (t) REVERT: A3 311 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4749 (tt0) REVERT: A3 330 CYS cc_start: 0.7728 (t) cc_final: 0.7468 (p) REVERT: A4 292 PHE cc_start: 0.6412 (m-80) cc_final: 0.6176 (m-80) REVERT: A4 330 CYS cc_start: 0.7755 (t) cc_final: 0.7380 (p) outliers start: 29 outliers final: 14 residues processed: 253 average time/residue: 1.7972 time to fit residues: 526.2294 Evaluate side-chains 185 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A2 residue 190 THR Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A2 residue 442 THR Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 173 SER Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 297 CYS Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 364 ASN Chi-restraints excluded: chain A4 residue 297 CYS Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 399 ASN A2 399 ASN A3 352 ASN A3 399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.197109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164070 restraints weight = 44396.831| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.83 r_work: 0.3805 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15636 Z= 0.156 Angle : 0.532 5.083 21216 Z= 0.300 Chirality : 0.039 0.141 2376 Planarity : 0.005 0.044 2636 Dihedral : 5.297 33.959 2030 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.39 % Allowed : 13.34 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.17 (0.19), residues: 1824 helix: 1.69 (0.15), residues: 1044 sheet: -0.18 (0.37), residues: 184 loop : -0.49 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPA2 375 HIS 0.004 0.002 HISA3 200 PHE 0.022 0.002 PHEA2 421 TYR 0.025 0.002 TYRA4 68 ARG 0.003 0.001 ARGA4 349 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 913) hydrogen bonds : angle 4.49636 ( 2652) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.50170 ( 8) covalent geometry : bond 0.00349 (15632) covalent geometry : angle 0.53157 (21208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4099 (OUTLIER) cc_final: 0.3524 (t80) REVERT: A1 330 CYS cc_start: 0.7759 (t) cc_final: 0.7363 (p) REVERT: A1 472 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: A2 330 CYS cc_start: 0.7723 (t) cc_final: 0.7495 (p) REVERT: A2 386 THR cc_start: 0.7023 (p) cc_final: 0.6820 (m) REVERT: A2 502 ASN cc_start: 0.7668 (t0) cc_final: 0.6994 (m-40) REVERT: A3 311 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.3732 (mp0) REVERT: A3 330 CYS cc_start: 0.7709 (t) cc_final: 0.7470 (p) REVERT: A3 472 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: A4 330 CYS cc_start: 0.7763 (t) cc_final: 0.7473 (p) REVERT: A4 386 THR cc_start: 0.7070 (p) cc_final: 0.6863 (m) outliers start: 40 outliers final: 26 residues processed: 216 average time/residue: 1.6269 time to fit residues: 414.0368 Evaluate side-chains 185 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 190 THR Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 461 ILE Chi-restraints excluded: chain A1 residue 472 GLU Chi-restraints excluded: chain A2 residue 190 THR Chi-restraints excluded: chain A2 residue 248 SER Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A2 residue 442 THR Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 173 SER Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 248 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 364 ASN Chi-restraints excluded: chain A3 residue 454 ILE Chi-restraints excluded: chain A3 residue 461 ILE Chi-restraints excluded: chain A3 residue 472 GLU Chi-restraints excluded: chain A4 residue 248 SER Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 297 CYS Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 442 THR Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 0.1980 chunk 70 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 352 ASN A3 399 ASN ** A4 251 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.194193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161539 restraints weight = 44540.412| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.81 r_work: 0.3787 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15636 Z= 0.174 Angle : 0.536 4.894 21216 Z= 0.301 Chirality : 0.040 0.141 2376 Planarity : 0.005 0.043 2636 Dihedral : 5.304 33.504 2030 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.93 % Allowed : 13.82 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.17 (0.19), residues: 1824 helix: 1.73 (0.15), residues: 1044 sheet: -0.14 (0.38), residues: 184 loop : -0.58 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPA2 375 HIS 0.005 0.002 HISA2 200 PHE 0.022 0.002 PHEA1 421 TYR 0.023 0.002 TYRA3 68 ARG 0.004 0.001 ARGA2 285 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 913) hydrogen bonds : angle 4.49099 ( 2652) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.40261 ( 8) covalent geometry : bond 0.00398 (15632) covalent geometry : angle 0.53596 (21208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4310 (OUTLIER) cc_final: 0.3583 (t80) REVERT: A1 330 CYS cc_start: 0.7676 (t) cc_final: 0.7315 (p) REVERT: A1 471 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: A2 60 TYR cc_start: 0.3973 (OUTLIER) cc_final: 0.3282 (t80) REVERT: A2 333 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7394 (t) REVERT: A2 502 ASN cc_start: 0.7683 (t0) cc_final: 0.7089 (m-40) REVERT: A3 60 TYR cc_start: 0.4086 (OUTLIER) cc_final: 0.2663 (t80) REVERT: A3 330 CYS cc_start: 0.7702 (t) cc_final: 0.7474 (p) REVERT: A4 60 TYR cc_start: 0.3947 (OUTLIER) cc_final: 0.2634 (t80) REVERT: A4 330 CYS cc_start: 0.7714 (t) cc_final: 0.7447 (p) REVERT: A4 386 THR cc_start: 0.7065 (p) cc_final: 0.6843 (m) outliers start: 49 outliers final: 30 residues processed: 216 average time/residue: 1.4255 time to fit residues: 369.3801 Evaluate side-chains 198 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 190 THR Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 461 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 190 THR Chi-restraints excluded: chain A2 residue 248 SER Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 333 VAL Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A2 residue 442 THR Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 173 SER Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 199 SER Chi-restraints excluded: chain A3 residue 248 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 364 ASN Chi-restraints excluded: chain A3 residue 454 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 139 VAL Chi-restraints excluded: chain A4 residue 185 THR Chi-restraints excluded: chain A4 residue 248 SER Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 442 THR Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 399 ASN ** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.195930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163546 restraints weight = 44407.886| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.79 r_work: 0.3826 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15636 Z= 0.151 Angle : 0.504 4.520 21216 Z= 0.283 Chirality : 0.038 0.140 2376 Planarity : 0.005 0.045 2636 Dihedral : 5.117 32.612 2030 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.81 % Allowed : 13.76 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.27 (0.19), residues: 1824 helix: 1.84 (0.15), residues: 1044 sheet: -0.25 (0.38), residues: 184 loop : -0.55 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPA3 114 HIS 0.004 0.002 HISA2 200 PHE 0.021 0.002 PHEA2 421 TYR 0.014 0.002 TYRA1 48 ARG 0.004 0.000 ARGA4 475 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 913) hydrogen bonds : angle 4.40868 ( 2652) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.38440 ( 8) covalent geometry : bond 0.00339 (15632) covalent geometry : angle 0.50424 (21208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4382 (OUTLIER) cc_final: 0.2749 (t80) REVERT: A1 330 CYS cc_start: 0.7711 (t) cc_final: 0.7382 (p) REVERT: A1 471 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A1 502 ASN cc_start: 0.7393 (t0) cc_final: 0.6429 (m-40) REVERT: A2 60 TYR cc_start: 0.4107 (OUTLIER) cc_final: 0.2672 (t80) REVERT: A2 502 ASN cc_start: 0.7617 (t0) cc_final: 0.7062 (m-40) REVERT: A3 60 TYR cc_start: 0.4169 (OUTLIER) cc_final: 0.2734 (t80) REVERT: A3 330 CYS cc_start: 0.7726 (t) cc_final: 0.7516 (p) REVERT: A4 60 TYR cc_start: 0.4080 (OUTLIER) cc_final: 0.2691 (t80) REVERT: A4 330 CYS cc_start: 0.7731 (t) cc_final: 0.7512 (p) REVERT: A4 386 THR cc_start: 0.7120 (p) cc_final: 0.6909 (m) outliers start: 47 outliers final: 31 residues processed: 213 average time/residue: 1.4163 time to fit residues: 364.0736 Evaluate side-chains 196 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 62 MET Chi-restraints excluded: chain A1 residue 134 ASN Chi-restraints excluded: chain A1 residue 190 THR Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 461 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 190 THR Chi-restraints excluded: chain A2 residue 248 SER Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A2 residue 442 THR Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 173 SER Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 199 SER Chi-restraints excluded: chain A3 residue 248 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 364 ASN Chi-restraints excluded: chain A3 residue 454 ILE Chi-restraints excluded: chain A3 residue 461 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 139 VAL Chi-restraints excluded: chain A4 residue 173 SER Chi-restraints excluded: chain A4 residue 248 SER Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 113 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159342 restraints weight = 44798.843| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.81 r_work: 0.3767 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15636 Z= 0.201 Angle : 0.554 5.023 21216 Z= 0.311 Chirality : 0.040 0.141 2376 Planarity : 0.005 0.048 2636 Dihedral : 5.253 33.461 2028 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.83 % Allowed : 13.52 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.15 (0.19), residues: 1824 helix: 1.74 (0.15), residues: 1044 sheet: -0.16 (0.38), residues: 184 loop : -0.63 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRPA1 187 HIS 0.006 0.003 HISA2 200 PHE 0.021 0.002 PHEA2 421 TYR 0.015 0.002 TYRA1 48 ARG 0.003 0.000 ARGA2 285 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 913) hydrogen bonds : angle 4.54964 ( 2652) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.33222 ( 8) covalent geometry : bond 0.00469 (15632) covalent geometry : angle 0.55411 (21208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4457 (OUTLIER) cc_final: 0.2780 (t80) REVERT: A1 330 CYS cc_start: 0.7705 (t) cc_final: 0.7396 (p) REVERT: A1 471 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: A1 498 LEU cc_start: 0.8045 (tt) cc_final: 0.7736 (mp) REVERT: A2 60 TYR cc_start: 0.4270 (OUTLIER) cc_final: 0.2703 (t80) REVERT: A2 502 ASN cc_start: 0.7714 (t0) cc_final: 0.7196 (m110) REVERT: A3 60 TYR cc_start: 0.4209 (OUTLIER) cc_final: 0.2721 (t80) REVERT: A3 330 CYS cc_start: 0.7690 (t) cc_final: 0.7485 (p) REVERT: A4 60 TYR cc_start: 0.4243 (OUTLIER) cc_final: 0.2731 (t80) REVERT: A4 330 CYS cc_start: 0.7697 (t) cc_final: 0.7484 (p) REVERT: A4 386 THR cc_start: 0.7136 (p) cc_final: 0.6933 (m) outliers start: 64 outliers final: 43 residues processed: 226 average time/residue: 1.5392 time to fit residues: 412.6898 Evaluate side-chains 212 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 83 VAL Chi-restraints excluded: chain A1 residue 134 ASN Chi-restraints excluded: chain A1 residue 139 VAL Chi-restraints excluded: chain A1 residue 190 THR Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 254 ILE Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 461 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 83 VAL Chi-restraints excluded: chain A2 residue 134 ASN Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 190 THR Chi-restraints excluded: chain A2 residue 248 SER Chi-restraints excluded: chain A2 residue 254 ILE Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 330 CYS Chi-restraints excluded: chain A2 residue 442 THR Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 83 VAL Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 134 ASN Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 171 VAL Chi-restraints excluded: chain A3 residue 173 SER Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 199 SER Chi-restraints excluded: chain A3 residue 248 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 364 ASN Chi-restraints excluded: chain A3 residue 461 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 83 VAL Chi-restraints excluded: chain A4 residue 134 ASN Chi-restraints excluded: chain A4 residue 139 VAL Chi-restraints excluded: chain A4 residue 171 VAL Chi-restraints excluded: chain A4 residue 173 SER Chi-restraints excluded: chain A4 residue 185 THR Chi-restraints excluded: chain A4 residue 248 SER Chi-restraints excluded: chain A4 residue 254 ILE Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 399 ASN A2 502 ASN ** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.191325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158893 restraints weight = 44709.855| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.80 r_work: 0.3764 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15636 Z= 0.198 Angle : 0.555 5.002 21216 Z= 0.311 Chirality : 0.040 0.147 2376 Planarity : 0.005 0.050 2636 Dihedral : 5.178 33.811 2024 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.53 % Allowed : 14.71 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.10 (0.19), residues: 1824 helix: 1.69 (0.15), residues: 1044 sheet: -0.10 (0.38), residues: 184 loop : -0.67 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRPA1 187 HIS 0.006 0.003 HISA1 200 PHE 0.021 0.002 PHEA4 421 TYR 0.017 0.002 TYRA1 48 ARG 0.006 0.001 ARGA2 72 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 913) hydrogen bonds : angle 4.55146 ( 2652) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.35501 ( 8) covalent geometry : bond 0.00459 (15632) covalent geometry : angle 0.55473 (21208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4491 (OUTLIER) cc_final: 0.2811 (t80) REVERT: A1 330 CYS cc_start: 0.7730 (t) cc_final: 0.7494 (p) REVERT: A1 471 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: A1 498 LEU cc_start: 0.8071 (tt) cc_final: 0.7763 (mp) REVERT: A2 60 TYR cc_start: 0.4344 (OUTLIER) cc_final: 0.2728 (t80) REVERT: A2 502 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7281 (m110) REVERT: A3 60 TYR cc_start: 0.4315 (OUTLIER) cc_final: 0.2769 (t80) REVERT: A3 281 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5484 (mt) REVERT: A4 60 TYR cc_start: 0.4369 (OUTLIER) cc_final: 0.2792 (t80) REVERT: A4 163 LYS cc_start: 0.6001 (mttt) cc_final: 0.4923 (mmmt) REVERT: A4 386 THR cc_start: 0.7176 (p) cc_final: 0.6943 (m) outliers start: 59 outliers final: 41 residues processed: 223 average time/residue: 1.5015 time to fit residues: 400.8501 Evaluate side-chains 216 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 83 VAL Chi-restraints excluded: chain A1 residue 134 ASN Chi-restraints excluded: chain A1 residue 139 VAL Chi-restraints excluded: chain A1 residue 190 THR Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 461 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 83 VAL Chi-restraints excluded: chain A2 residue 89 THR Chi-restraints excluded: chain A2 residue 134 ASN Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 190 THR Chi-restraints excluded: chain A2 residue 248 SER Chi-restraints excluded: chain A2 residue 254 ILE Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A2 residue 442 THR Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A2 residue 502 ASN Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 83 VAL Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 134 ASN Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 173 SER Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 248 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 281 LEU Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 364 ASN Chi-restraints excluded: chain A3 residue 461 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 83 VAL Chi-restraints excluded: chain A4 residue 134 ASN Chi-restraints excluded: chain A4 residue 139 VAL Chi-restraints excluded: chain A4 residue 171 VAL Chi-restraints excluded: chain A4 residue 173 SER Chi-restraints excluded: chain A4 residue 248 SER Chi-restraints excluded: chain A4 residue 254 ILE Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 156 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 502 ASN A3 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163856 restraints weight = 44532.103| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.78 r_work: 0.3823 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15636 Z= 0.108 Angle : 0.461 4.557 21216 Z= 0.256 Chirality : 0.037 0.137 2376 Planarity : 0.004 0.046 2636 Dihedral : 4.728 31.730 2024 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.85 % Allowed : 15.97 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.46 (0.19), residues: 1824 helix: 2.03 (0.15), residues: 1048 sheet: -0.36 (0.37), residues: 184 loop : -0.47 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPA4 276 HIS 0.002 0.001 HISA4 200 PHE 0.018 0.001 PHEA4 421 TYR 0.025 0.001 TYRA2 68 ARG 0.003 0.000 ARGA2 285 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 913) hydrogen bonds : angle 4.24455 ( 2652) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.47936 ( 8) covalent geometry : bond 0.00228 (15632) covalent geometry : angle 0.46087 (21208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.2702 (t80) REVERT: A1 330 CYS cc_start: 0.7710 (t) cc_final: 0.7496 (p) REVERT: A1 471 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: A1 498 LEU cc_start: 0.7974 (tt) cc_final: 0.7685 (mp) REVERT: A2 60 TYR cc_start: 0.4217 (OUTLIER) cc_final: 0.2670 (t80) REVERT: A3 60 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.2714 (t80) REVERT: A3 281 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5407 (mt) REVERT: A4 60 TYR cc_start: 0.4239 (OUTLIER) cc_final: 0.2723 (t80) REVERT: A4 163 LYS cc_start: 0.5982 (mttt) cc_final: 0.4895 (mmmt) outliers start: 31 outliers final: 17 residues processed: 199 average time/residue: 1.5016 time to fit residues: 356.2028 Evaluate side-chains 192 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 330 CYS Chi-restraints excluded: chain A2 residue 343 ILE Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 281 LEU Chi-restraints excluded: chain A3 residue 297 CYS Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 173 SER Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 502 ASN ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 502 ASN A3 502 ASN ** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 502 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162638 restraints weight = 44399.625| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.78 r_work: 0.3808 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15636 Z= 0.127 Angle : 0.473 4.558 21216 Z= 0.263 Chirality : 0.038 0.138 2376 Planarity : 0.004 0.046 2636 Dihedral : 4.677 32.120 2022 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.73 % Allowed : 16.39 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.52 (0.20), residues: 1824 helix: 2.09 (0.15), residues: 1048 sheet: -0.34 (0.37), residues: 184 loop : -0.48 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPA3 114 HIS 0.003 0.001 HISA1 200 PHE 0.019 0.001 PHEA2 421 TYR 0.021 0.002 TYRA1 68 ARG 0.003 0.000 ARGA2 285 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 913) hydrogen bonds : angle 4.26094 ( 2652) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.34477 ( 8) covalent geometry : bond 0.00280 (15632) covalent geometry : angle 0.47328 (21208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4358 (OUTLIER) cc_final: 0.2682 (t80) REVERT: A1 330 CYS cc_start: 0.7705 (t) cc_final: 0.7471 (p) REVERT: A1 471 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A1 498 LEU cc_start: 0.7961 (tt) cc_final: 0.7685 (mp) REVERT: A2 60 TYR cc_start: 0.4200 (OUTLIER) cc_final: 0.2645 (t80) REVERT: A2 502 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7297 (m-40) REVERT: A3 60 TYR cc_start: 0.4130 (OUTLIER) cc_final: 0.2670 (t80) REVERT: A3 281 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5422 (mt) REVERT: A4 60 TYR cc_start: 0.4207 (OUTLIER) cc_final: 0.2692 (t80) REVERT: A4 68 TYR cc_start: 0.7511 (t80) cc_final: 0.7311 (t80) REVERT: A4 163 LYS cc_start: 0.5962 (mttt) cc_final: 0.4864 (mmmt) outliers start: 29 outliers final: 21 residues processed: 193 average time/residue: 1.5151 time to fit residues: 347.7495 Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 139 VAL Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 134 ASN Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 330 CYS Chi-restraints excluded: chain A2 residue 502 ASN Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 281 LEU Chi-restraints excluded: chain A3 residue 297 CYS Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 134 ASN Chi-restraints excluded: chain A4 residue 173 SER Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 343 ILE Chi-restraints excluded: chain A4 residue 461 ILE Chi-restraints excluded: chain A4 residue 502 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 122 optimal weight: 0.0020 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 502 ASN A3 346 ASN ** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162569 restraints weight = 44537.391| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.79 r_work: 0.3806 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.366 15636 Z= 0.245 Angle : 0.750 59.188 21216 Z= 0.482 Chirality : 0.040 0.641 2376 Planarity : 0.005 0.165 2636 Dihedral : 4.681 32.058 2022 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.67 % Allowed : 16.39 % Favored : 81.94 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1824 helix: 2.08 (0.15), residues: 1048 sheet: -0.35 (0.37), residues: 184 loop : -0.48 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPA3 114 HIS 0.002 0.001 HISA1 200 PHE 0.019 0.001 PHEA2 421 TYR 0.019 0.001 TYRA1 68 ARG 0.003 0.000 ARGA2 285 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 913) hydrogen bonds : angle 4.26268 ( 2652) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.32775 ( 8) covalent geometry : bond 0.00495 (15632) covalent geometry : angle 0.74995 (21208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 60 TYR cc_start: 0.4368 (OUTLIER) cc_final: 0.2679 (t80) REVERT: A1 330 CYS cc_start: 0.7698 (t) cc_final: 0.7461 (p) REVERT: A1 471 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: A1 498 LEU cc_start: 0.7962 (tt) cc_final: 0.7683 (mp) REVERT: A2 60 TYR cc_start: 0.4185 (OUTLIER) cc_final: 0.2634 (t80) REVERT: A3 60 TYR cc_start: 0.4128 (OUTLIER) cc_final: 0.2661 (t80) REVERT: A3 281 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5419 (mt) REVERT: A4 60 TYR cc_start: 0.4189 (OUTLIER) cc_final: 0.2690 (t80) REVERT: A4 68 TYR cc_start: 0.7509 (t80) cc_final: 0.7309 (t80) REVERT: A4 163 LYS cc_start: 0.5958 (mttt) cc_final: 0.4861 (mmmt) outliers start: 28 outliers final: 21 residues processed: 187 average time/residue: 1.5863 time to fit residues: 357.8434 Evaluate side-chains 191 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 TYR Chi-restraints excluded: chain A1 residue 139 VAL Chi-restraints excluded: chain A1 residue 248 SER Chi-restraints excluded: chain A1 residue 275 SER Chi-restraints excluded: chain A1 residue 343 ILE Chi-restraints excluded: chain A1 residue 471 GLU Chi-restraints excluded: chain A2 residue 60 TYR Chi-restraints excluded: chain A2 residue 134 ASN Chi-restraints excluded: chain A2 residue 139 VAL Chi-restraints excluded: chain A2 residue 275 SER Chi-restraints excluded: chain A2 residue 330 CYS Chi-restraints excluded: chain A2 residue 461 ILE Chi-restraints excluded: chain A3 residue 60 TYR Chi-restraints excluded: chain A3 residue 130 ILE Chi-restraints excluded: chain A3 residue 139 VAL Chi-restraints excluded: chain A3 residue 198 SER Chi-restraints excluded: chain A3 residue 275 SER Chi-restraints excluded: chain A3 residue 281 LEU Chi-restraints excluded: chain A3 residue 297 CYS Chi-restraints excluded: chain A3 residue 311 GLU Chi-restraints excluded: chain A3 residue 343 ILE Chi-restraints excluded: chain A3 residue 461 ILE Chi-restraints excluded: chain A4 residue 60 TYR Chi-restraints excluded: chain A4 residue 134 ASN Chi-restraints excluded: chain A4 residue 173 SER Chi-restraints excluded: chain A4 residue 275 SER Chi-restraints excluded: chain A4 residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 180 optimal weight: 0.0170 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 346 ASN ** A4 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.194831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162755 restraints weight = 44417.186| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.78 r_work: 0.3806 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.366 15636 Z= 0.245 Angle : 0.750 59.188 21216 Z= 0.482 Chirality : 0.040 0.641 2376 Planarity : 0.005 0.165 2636 Dihedral : 4.681 32.058 2022 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.61 % Allowed : 16.33 % Favored : 82.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1824 helix: 2.08 (0.15), residues: 1048 sheet: -0.35 (0.37), residues: 184 loop : -0.48 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPA3 114 HIS 0.002 0.001 HISA1 200 PHE 0.019 0.001 PHEA2 421 TYR 0.019 0.001 TYRA1 68 ARG 0.003 0.000 ARGA2 285 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 913) hydrogen bonds : angle 4.26268 ( 2652) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.32775 ( 8) covalent geometry : bond 0.00495 (15632) covalent geometry : angle 0.74995 (21208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19817.23 seconds wall clock time: 343 minutes 46.45 seconds (20626.45 seconds total)