Starting phenix.real_space_refine on Wed Mar 4 05:44:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlb_22238/03_2026/6xlb_22238.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlb_22238/03_2026/6xlb_22238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlb_22238/03_2026/6xlb_22238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlb_22238/03_2026/6xlb_22238.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlb_22238/03_2026/6xlb_22238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlb_22238/03_2026/6xlb_22238.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7178 2.51 5 N 1828 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11180 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3304 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3304 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 15, 'TRANS': 390} Chain: "C1" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Chain: "D1" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Time building chain proxies: 2.69, per 1000 atoms: 0.24 Number of scatterers: 11180 At special positions: 0 Unit cell: (97.008, 107.328, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2152 8.00 N 1828 7.00 C 7178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 601.2 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.582A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.955A pdb=" N VAL A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 4.188A pdb=" N LYS A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.614A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 removed outlier: 4.287A pdb=" N ALA A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.842A pdb=" N LYS A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 651 Processing helix chain 'A' and resid 656 through 672 removed outlier: 4.392A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.501A pdb=" N THR B 274 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.523A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 3.700A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.800A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 484 through 490 Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.591A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.532A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.603A pdb=" N ALA B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 651 Processing helix chain 'B' and resid 656 through 672 removed outlier: 4.139A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C1' and resid 16 through 28 Processing helix chain 'C1' and resid 117 through 121 Processing helix chain 'C1' and resid 122 through 131 removed outlier: 3.631A pdb=" N LEUC1 126 " --> pdb=" O GLUC1 122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILEC1 127 " --> pdb=" O ALAC1 123 " (cutoff:3.500A) Processing helix chain 'C1' and resid 131 through 150 removed outlier: 3.916A pdb=" N GLYC1 143 " --> pdb=" O PHEC1 139 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSC1 144 " --> pdb=" O GLNC1 140 " (cutoff:3.500A) Processing helix chain 'C1' and resid 225 through 233 Processing helix chain 'C1' and resid 235 through 244 Processing helix chain 'C1' and resid 326 through 336 Processing helix chain 'C1' and resid 337 through 344 Processing helix chain 'D1' and resid 16 through 28 Processing helix chain 'D1' and resid 117 through 121 Processing helix chain 'D1' and resid 122 through 131 removed outlier: 3.994A pdb=" N LEUD1 126 " --> pdb=" O GLUD1 122 " (cutoff:3.500A) Processing helix chain 'D1' and resid 131 through 150 removed outlier: 3.910A pdb=" N GLYD1 143 " --> pdb=" O PHED1 139 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYSD1 144 " --> pdb=" O GLND1 140 " (cutoff:3.500A) Processing helix chain 'D1' and resid 225 through 233 Processing helix chain 'D1' and resid 235 through 244 Processing helix chain 'D1' and resid 324 through 336 Processing helix chain 'D1' and resid 337 through 344 Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.619A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.321A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 563 removed outlier: 7.828A pdb=" N PHE A 609 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 561 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 611 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 563 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 307 removed outlier: 6.349A pdb=" N LYS B 338 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER B 367 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 340 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 451 through 452 removed outlier: 4.182A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.690A pdb=" N LYS B 560 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 611 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 562 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C1' and resid 13 through 15 Processing sheet with id=AA8, first strand: chain 'C1' and resid 41 through 53 removed outlier: 7.073A pdb=" N LEUC1 74 " --> pdb=" O LYSC1 45 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VALC1 47 " --> pdb=" O THRC1 72 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THRC1 72 " --> pdb=" O VALC1 47 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SERC1 49 " --> pdb=" O LYSC1 70 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSC1 70 " --> pdb=" O SERC1 49 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLUC1 51 " --> pdb=" O ASPC1 68 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASPC1 68 " --> pdb=" O GLUC1 51 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEUC1 69 " --> pdb=" O GLUC1 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLUC1 97 " --> pdb=" O LEUC1 69 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLUC1 90 " --> pdb=" O PHEC1 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C1' and resid 213 through 218 removed outlier: 6.941A pdb=" N ILEC1 216 " --> pdb=" O THRC1 318 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THRC1 318 " --> pdb=" O ILEC1 216 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEUC1 218 " --> pdb=" O LYSC1 316 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYSC1 316 " --> pdb=" O LEUC1 218 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SERC1 274 " --> pdb=" O VALC1 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C1' and resid 213 through 218 removed outlier: 6.941A pdb=" N ILEC1 216 " --> pdb=" O THRC1 318 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THRC1 318 " --> pdb=" O ILEC1 216 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEUC1 218 " --> pdb=" O LYSC1 316 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYSC1 316 " --> pdb=" O LEUC1 218 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SERC1 274 " --> pdb=" O VALC1 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C1' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain 'D1' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'D1' and resid 41 through 53 removed outlier: 8.051A pdb=" N LYSD1 43 " --> pdb=" O HISD1 78 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N HISD1 78 " --> pdb=" O LYSD1 43 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYSD1 45 " --> pdb=" O GLUD1 76 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLUD1 76 " --> pdb=" O LYSD1 45 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VALD1 47 " --> pdb=" O LEUD1 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEUD1 74 " --> pdb=" O VALD1 47 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEUD1 69 " --> pdb=" O GLUD1 97 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLUD1 97 " --> pdb=" O LEUD1 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D1' and resid 214 through 218 removed outlier: 5.248A pdb=" N THRD1 214 " --> pdb=" O GLYD1 319 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N HISD1 284 " --> pdb=" O LEUD1 272 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEUD1 272 " --> pdb=" O HISD1 284 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYSD1 286 " --> pdb=" O SERD1 270 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SERD1 270 " --> pdb=" O LYSD1 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D1' and resid 221 through 222 512 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3581 1.34 - 1.46: 2506 1.46 - 1.58: 5281 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 11406 Sorted by residual: bond pdb=" CA GLU A 544 " pdb=" C GLU A 544 " ideal model delta sigma weight residual 1.521 1.529 -0.008 1.14e-02 7.69e+03 5.05e-01 bond pdb=" CA GLU A 656 " pdb=" CB GLU A 656 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.58e-02 4.01e+03 4.65e-01 bond pdb=" CA ASP A 637 " pdb=" CB ASP A 637 " ideal model delta sigma weight residual 1.528 1.539 -0.010 1.66e-02 3.63e+03 3.90e-01 bond pdb=" CB GLU A 656 " pdb=" CG GLU A 656 " ideal model delta sigma weight residual 1.520 1.537 -0.017 3.00e-02 1.11e+03 3.09e-01 bond pdb=" C GLU A 544 " pdb=" O GLU A 544 " ideal model delta sigma weight residual 1.244 1.238 0.005 1.00e-02 1.00e+04 2.98e-01 ... (remaining 11401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 15032 1.19 - 2.38: 264 2.38 - 3.57: 50 3.57 - 4.76: 12 4.76 - 5.95: 8 Bond angle restraints: 15366 Sorted by residual: angle pdb=" C TYR A 543 " pdb=" N GLU A 544 " pdb=" CA GLU A 544 " ideal model delta sigma weight residual 119.78 122.50 -2.72 1.24e+00 6.50e-01 4.81e+00 angle pdb=" CA GLU A 656 " pdb=" CB GLU A 656 " pdb=" CG GLU A 656 " ideal model delta sigma weight residual 114.10 117.93 -3.83 2.00e+00 2.50e-01 3.66e+00 angle pdb=" CA TRPC1 242 " pdb=" CB TRPC1 242 " pdb=" CG TRPC1 242 " ideal model delta sigma weight residual 113.60 117.21 -3.61 1.90e+00 2.77e-01 3.61e+00 angle pdb=" C LEU A 509 " pdb=" N LYS A 510 " pdb=" CA LYS A 510 " ideal model delta sigma weight residual 121.54 125.05 -3.51 1.91e+00 2.74e-01 3.38e+00 angle pdb=" C LEU B 509 " pdb=" N LYS B 510 " pdb=" CA LYS B 510 " ideal model delta sigma weight residual 121.54 124.88 -3.34 1.91e+00 2.74e-01 3.05e+00 ... (remaining 15361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6418 17.95 - 35.90: 415 35.90 - 53.85: 81 53.85 - 71.80: 23 71.80 - 89.75: 19 Dihedral angle restraints: 6956 sinusoidal: 2902 harmonic: 4054 Sorted by residual: dihedral pdb=" CB GLUC1 228 " pdb=" CG GLUC1 228 " pdb=" CD GLUC1 228 " pdb=" OE1 GLUC1 228 " ideal model delta sinusoidal sigma weight residual 0.00 -86.78 86.78 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA ASNC1 152 " pdb=" CB ASNC1 152 " pdb=" CG ASNC1 152 " pdb=" OD1 ASNC1 152 " ideal model delta sinusoidal sigma weight residual 120.00 -174.79 -65.21 2 2.00e+01 2.50e-03 9.89e+00 dihedral pdb=" CB GLUD1 324 " pdb=" CG GLUD1 324 " pdb=" CD GLUD1 324 " pdb=" OE1 GLUD1 324 " ideal model delta sinusoidal sigma weight residual 0.00 84.92 -84.92 1 3.00e+01 1.11e-03 9.72e+00 ... (remaining 6953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1031 0.029 - 0.058: 438 0.058 - 0.086: 112 0.086 - 0.115: 100 0.115 - 0.144: 13 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILEC1 50 " pdb=" N ILEC1 50 " pdb=" C ILEC1 50 " pdb=" CB ILEC1 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1691 not shown) Planarity restraints: 1960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALD1 224 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PROD1 225 " -0.062 5.00e-02 4.00e+02 pdb=" CA PROD1 225 " 0.018 5.00e-02 4.00e+02 pdb=" CD PROD1 225 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALC1 224 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PROC1 225 " 0.054 5.00e-02 4.00e+02 pdb=" CA PROC1 225 " -0.016 5.00e-02 4.00e+02 pdb=" CD PROC1 225 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 355 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.017 5.00e-02 4.00e+02 ... (remaining 1957 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1964 2.77 - 3.30: 10804 3.30 - 3.83: 18776 3.83 - 4.37: 22534 4.37 - 4.90: 38408 Nonbonded interactions: 92486 Sorted by model distance: nonbonded pdb=" OE1 GLU B 586 " pdb=" OG SER B 604 " model vdw 2.235 3.040 nonbonded pdb=" O ILEC1 239 " pdb=" OG1 THRC1 243 " model vdw 2.243 3.040 nonbonded pdb=" O ILED1 239 " pdb=" OG1 THRD1 243 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" O GLU A 493 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 446 " pdb=" O GLU B 449 " model vdw 2.255 3.040 ... (remaining 92481 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C1' selection = chain 'D1' } 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 group one per residue 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: 2.540 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.002 0.021 11406 Z= 0.081 Angle : 0.428 5.953 15366 Z= 0.238 Chirality : 0.040 0.144 1694 Planarity : 0.003 0.036 1960 Dihedral : 13.651 89.751 4316 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.20), residues: 1368 helix: -1.42 (0.20), residues: 518 sheet: -1.62 (0.29), residues: 284 loop : -1.58 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGC1 329 TYR 0.005 0.001 TYR A 469 PHE 0.008 0.001 PHE B 579 TRP 0.015 0.001 TRPC1 242 HIS 0.004 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00150 (11406) covalent geometry : angle 0.42784 (15366) hydrogen bonds : bond 0.15424 ( 497) hydrogen bonds : angle 6.20015 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.424 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.9046 (mt) cc_final: 0.8739 (tt) REVERT: A 396 LEU cc_start: 0.9558 (mt) cc_final: 0.9345 (mt) REVERT: A 493 GLU cc_start: 0.6227 (tt0) cc_final: 0.5832 (tt0) REVERT: A 523 ASP cc_start: 0.7776 (t0) cc_final: 0.7573 (t0) REVERT: A 599 MET cc_start: 0.5479 (tpt) cc_final: 0.4985 (ppp) REVERT: B 581 TRP cc_start: 0.5357 (m-10) cc_final: 0.5110 (m-90) REVERT: B 599 MET cc_start: 0.5452 (tpp) cc_final: 0.4776 (tmm) REVERT: B 640 ASN cc_start: 0.8149 (t0) cc_final: 0.7871 (t0) REVERT: C1 26 GLN cc_start: 0.8362 (tp40) cc_final: 0.8156 (tp40) REVERT: C1 94 ASN cc_start: 0.8382 (p0) cc_final: 0.8161 (p0) REVERT: C1 138 ILE cc_start: 0.8931 (mt) cc_final: 0.8481 (mt) REVERT: C1 317 TRP cc_start: 0.8231 (t60) cc_final: 0.7912 (t60) REVERT: D1 23 TYR cc_start: 0.6977 (t80) cc_final: 0.6375 (t80) REVERT: D1 70 LYS cc_start: 0.7652 (tttt) cc_final: 0.6976 (ttpp) REVERT: D1 271 GLU cc_start: 0.7314 (tt0) cc_final: 0.6870 (tt0) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1420 time to fit residues: 66.2286 Evaluate side-chains 202 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 430 GLN A 442 ASN A 466 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 508 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN C1 212 ASN D1 78 HIS D1 284 HIS ** D1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.082363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067870 restraints weight = 38277.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069979 restraints weight = 22840.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071432 restraints weight = 16078.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072446 restraints weight = 12573.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073174 restraints weight = 10507.916| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11406 Z= 0.212 Angle : 0.631 7.799 15366 Z= 0.333 Chirality : 0.046 0.195 1694 Planarity : 0.004 0.045 1960 Dihedral : 3.862 17.396 1466 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.09 % Allowed : 12.80 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.22), residues: 1368 helix: -0.11 (0.23), residues: 524 sheet: -1.20 (0.29), residues: 278 loop : -1.03 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 322 TYR 0.022 0.002 TYRD1 335 PHE 0.021 0.002 PHE A 288 TRP 0.027 0.003 TRP B 296 HIS 0.010 0.002 HISD1 309 Details of bonding type rmsd covalent geometry : bond 0.00462 (11406) covalent geometry : angle 0.63113 (15366) hydrogen bonds : bond 0.03455 ( 497) hydrogen bonds : angle 5.16934 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.478 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 revert: symmetry clash REVERT: A 385 MET cc_start: 0.7944 (tmm) cc_final: 0.7312 (tmm) REVERT: A 396 LEU cc_start: 0.9751 (mt) cc_final: 0.9540 (mm) REVERT: A 523 ASP cc_start: 0.8290 (t0) cc_final: 0.8046 (t0) REVERT: A 599 MET cc_start: 0.5893 (tpt) cc_final: 0.5522 (ppp) REVERT: B 385 MET cc_start: 0.8582 (tmm) cc_final: 0.8309 (tmm) REVERT: B 599 MET cc_start: 0.5745 (tpp) cc_final: 0.4856 (tmm) REVERT: C1 231 GLU cc_start: 0.8247 (mp0) cc_final: 0.7955 (mp0) REVERT: C1 250 ASN cc_start: 0.8194 (m-40) cc_final: 0.7661 (m110) REVERT: C1 317 TRP cc_start: 0.8746 (t60) cc_final: 0.8328 (t60) REVERT: C1 331 ASN cc_start: 0.8733 (m110) cc_final: 0.8515 (m110) REVERT: C1 335 TYR cc_start: 0.8186 (m-80) cc_final: 0.7878 (m-10) REVERT: D1 271 GLU cc_start: 0.8264 (tt0) cc_final: 0.7500 (tt0) REVERT: D1 312 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8126 (ttpp) REVERT: D1 331 ASN cc_start: 0.8847 (m110) cc_final: 0.8625 (m110) outliers start: 26 outliers final: 15 residues processed: 209 average time/residue: 0.1274 time to fit residues: 36.5621 Evaluate side-chains 167 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 66 LEU Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 212 ASN Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.067792 restraints weight = 38434.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069897 restraints weight = 22991.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071390 restraints weight = 16264.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072374 restraints weight = 12728.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073137 restraints weight = 10716.800| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11406 Z= 0.131 Angle : 0.583 8.938 15366 Z= 0.302 Chirality : 0.044 0.166 1694 Planarity : 0.004 0.043 1960 Dihedral : 3.958 18.099 1466 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.22), residues: 1368 helix: 0.05 (0.23), residues: 528 sheet: -0.98 (0.29), residues: 298 loop : -0.83 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGD1 338 TYR 0.017 0.002 TYRD1 335 PHE 0.042 0.001 PHE B 400 TRP 0.040 0.002 TRP B 296 HIS 0.007 0.001 HISD1 309 Details of bonding type rmsd covalent geometry : bond 0.00293 (11406) covalent geometry : angle 0.58320 (15366) hydrogen bonds : bond 0.03151 ( 497) hydrogen bonds : angle 4.97016 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.462 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: A 460 MET cc_start: 0.8077 (mmm) cc_final: 0.7708 (mmm) REVERT: A 523 ASP cc_start: 0.8271 (t0) cc_final: 0.8016 (t0) REVERT: A 546 LEU cc_start: 0.8916 (mt) cc_final: 0.8678 (mt) REVERT: A 599 MET cc_start: 0.6029 (tpt) cc_final: 0.5504 (ppp) REVERT: B 385 MET cc_start: 0.8528 (tmm) cc_final: 0.8290 (tmm) REVERT: B 599 MET cc_start: 0.5655 (tpp) cc_final: 0.4699 (tmm) REVERT: B 644 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7844 (mp0) REVERT: C1 25 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8318 (mttm) REVERT: C1 94 ASN cc_start: 0.8779 (p0) cc_final: 0.8548 (p0) REVERT: C1 217 TYR cc_start: 0.9079 (t80) cc_final: 0.8775 (t80) REVERT: C1 231 GLU cc_start: 0.8266 (mp0) cc_final: 0.7936 (mp0) REVERT: C1 238 ARG cc_start: 0.8355 (mtm180) cc_final: 0.7969 (mtm180) REVERT: C1 271 GLU cc_start: 0.7040 (tp30) cc_final: 0.6786 (tp30) REVERT: C1 317 TRP cc_start: 0.8771 (t60) cc_final: 0.8496 (t60) REVERT: C1 331 ASN cc_start: 0.8786 (m110) cc_final: 0.8530 (m110) REVERT: C1 335 TYR cc_start: 0.8063 (m-80) cc_final: 0.7804 (m-10) REVERT: D1 271 GLU cc_start: 0.8244 (tt0) cc_final: 0.7657 (tt0) REVERT: D1 308 PHE cc_start: 0.8423 (m-10) cc_final: 0.8150 (m-10) REVERT: D1 314 GLN cc_start: 0.8956 (pt0) cc_final: 0.8555 (pt0) REVERT: D1 331 ASN cc_start: 0.8797 (m110) cc_final: 0.8521 (m110) outliers start: 23 outliers final: 17 residues processed: 202 average time/residue: 0.1162 time to fit residues: 33.1514 Evaluate side-chains 170 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 304 GLU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 381 GLN B 310 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 58 GLN ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067118 restraints weight = 38749.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069232 restraints weight = 22824.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070686 restraints weight = 16037.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071680 restraints weight = 12568.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072436 restraints weight = 10550.962| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11406 Z= 0.128 Angle : 0.576 8.844 15366 Z= 0.298 Chirality : 0.044 0.198 1694 Planarity : 0.004 0.041 1960 Dihedral : 4.051 21.201 1466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.90 % Allowed : 15.46 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.22), residues: 1368 helix: 0.20 (0.23), residues: 528 sheet: -0.87 (0.29), residues: 298 loop : -0.77 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGC1 329 TYR 0.015 0.001 TYRD1 335 PHE 0.031 0.001 PHE B 400 TRP 0.033 0.002 TRP A 296 HIS 0.010 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00294 (11406) covalent geometry : angle 0.57560 (15366) hydrogen bonds : bond 0.03012 ( 497) hydrogen bonds : angle 4.90000 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.454 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: A 523 ASP cc_start: 0.8219 (t0) cc_final: 0.7947 (t0) REVERT: A 546 LEU cc_start: 0.8969 (mt) cc_final: 0.8707 (mt) REVERT: A 599 MET cc_start: 0.6037 (tpt) cc_final: 0.5542 (ppp) REVERT: B 385 MET cc_start: 0.8545 (tmm) cc_final: 0.8311 (tmm) REVERT: B 599 MET cc_start: 0.5707 (tpp) cc_final: 0.4760 (tmm) REVERT: B 644 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7766 (mp0) REVERT: C1 94 ASN cc_start: 0.8796 (p0) cc_final: 0.8496 (p0) REVERT: C1 217 TYR cc_start: 0.9133 (t80) cc_final: 0.8195 (t80) REVERT: C1 231 GLU cc_start: 0.8225 (mp0) cc_final: 0.7869 (mp0) REVERT: C1 271 GLU cc_start: 0.7098 (tp30) cc_final: 0.6808 (tp30) REVERT: C1 314 GLN cc_start: 0.8959 (tt0) cc_final: 0.8195 (tt0) REVERT: C1 317 TRP cc_start: 0.8761 (t60) cc_final: 0.8559 (t60) REVERT: C1 331 ASN cc_start: 0.8818 (m110) cc_final: 0.8483 (m110) REVERT: D1 271 GLU cc_start: 0.8234 (tt0) cc_final: 0.7646 (tt0) REVERT: D1 308 PHE cc_start: 0.8396 (m-10) cc_final: 0.7932 (m-10) REVERT: D1 314 GLN cc_start: 0.8977 (pt0) cc_final: 0.8524 (pt0) REVERT: D1 331 ASN cc_start: 0.8813 (m110) cc_final: 0.8535 (m110) outliers start: 36 outliers final: 21 residues processed: 191 average time/residue: 0.1111 time to fit residues: 30.2383 Evaluate side-chains 165 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 97 GLU Chi-restraints excluded: chain C1 residue 304 GLU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 349 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.080738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066203 restraints weight = 38523.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068241 restraints weight = 22958.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069695 restraints weight = 16259.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070679 restraints weight = 12771.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.071394 restraints weight = 10736.049| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11406 Z= 0.133 Angle : 0.572 12.132 15366 Z= 0.294 Chirality : 0.044 0.159 1694 Planarity : 0.004 0.039 1960 Dihedral : 4.043 21.400 1466 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.85 % Allowed : 17.39 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1368 helix: 0.24 (0.23), residues: 530 sheet: -0.78 (0.30), residues: 300 loop : -0.72 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGD1 329 TYR 0.024 0.002 TYRC1 335 PHE 0.024 0.001 PHE B 400 TRP 0.033 0.002 TRP A 296 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00298 (11406) covalent geometry : angle 0.57186 (15366) hydrogen bonds : bond 0.02907 ( 497) hydrogen bonds : angle 4.84758 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.492 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: A 523 ASP cc_start: 0.8226 (t0) cc_final: 0.7962 (t0) REVERT: A 546 LEU cc_start: 0.9039 (mt) cc_final: 0.8814 (mt) REVERT: A 589 MET cc_start: 0.8218 (ptm) cc_final: 0.7408 (ptm) REVERT: A 599 MET cc_start: 0.6070 (tpt) cc_final: 0.5606 (ppp) REVERT: B 385 MET cc_start: 0.8509 (tmm) cc_final: 0.8272 (tmm) REVERT: B 520 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8802 (tt) REVERT: B 599 MET cc_start: 0.5853 (tpp) cc_final: 0.4964 (tmm) REVERT: B 644 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7800 (mp0) REVERT: C1 94 ASN cc_start: 0.8804 (p0) cc_final: 0.8532 (p0) REVERT: C1 231 GLU cc_start: 0.8187 (mp0) cc_final: 0.7874 (mp0) REVERT: C1 331 ASN cc_start: 0.8787 (m110) cc_final: 0.8545 (m110) REVERT: D1 271 GLU cc_start: 0.8243 (tt0) cc_final: 0.7708 (tt0) REVERT: D1 308 PHE cc_start: 0.8341 (m-10) cc_final: 0.7931 (m-10) REVERT: D1 331 ASN cc_start: 0.8819 (m110) cc_final: 0.8526 (m110) outliers start: 23 outliers final: 18 residues processed: 167 average time/residue: 0.1128 time to fit residues: 26.6452 Evaluate side-chains 154 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 97 GLU Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 304 GLU Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.081153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066358 restraints weight = 38567.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068454 restraints weight = 23079.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069916 restraints weight = 16312.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070941 restraints weight = 12773.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071676 restraints weight = 10749.150| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11406 Z= 0.118 Angle : 0.576 9.007 15366 Z= 0.296 Chirality : 0.044 0.194 1694 Planarity : 0.003 0.038 1960 Dihedral : 3.992 20.610 1466 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.82 % Allowed : 18.20 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1368 helix: 0.26 (0.23), residues: 532 sheet: -0.71 (0.31), residues: 284 loop : -0.75 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGD1 329 TYR 0.028 0.002 TYRC1 217 PHE 0.027 0.001 PHEC1 261 TRP 0.034 0.002 TRP A 296 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00267 (11406) covalent geometry : angle 0.57553 (15366) hydrogen bonds : bond 0.02882 ( 497) hydrogen bonds : angle 4.81969 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.469 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: A 523 ASP cc_start: 0.8197 (t0) cc_final: 0.7928 (t0) REVERT: A 546 LEU cc_start: 0.9039 (mt) cc_final: 0.8802 (mt) REVERT: A 585 MET cc_start: 0.8091 (tmm) cc_final: 0.6788 (tmm) REVERT: A 599 MET cc_start: 0.6107 (tpt) cc_final: 0.5625 (ppp) REVERT: B 385 MET cc_start: 0.8437 (tmm) cc_final: 0.7999 (tmm) REVERT: B 599 MET cc_start: 0.6037 (tpp) cc_final: 0.5115 (tmm) REVERT: B 644 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7833 (mp0) REVERT: C1 70 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7932 (tptt) REVERT: C1 94 ASN cc_start: 0.8813 (p0) cc_final: 0.8269 (p0) REVERT: C1 217 TYR cc_start: 0.9087 (t80) cc_final: 0.8885 (t80) REVERT: C1 231 GLU cc_start: 0.8149 (mp0) cc_final: 0.7834 (mp0) REVERT: C1 331 ASN cc_start: 0.8849 (m110) cc_final: 0.8616 (m110) REVERT: D1 60 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7747 (mttp) REVERT: D1 212 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7704 (t0) REVERT: D1 271 GLU cc_start: 0.8241 (tt0) cc_final: 0.7697 (tt0) REVERT: D1 299 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: D1 308 PHE cc_start: 0.8296 (m-10) cc_final: 0.7975 (m-10) REVERT: D1 331 ASN cc_start: 0.8783 (m110) cc_final: 0.8453 (m110) outliers start: 35 outliers final: 23 residues processed: 176 average time/residue: 0.1088 time to fit residues: 27.4707 Evaluate side-chains 162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 70 LYS Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 97 GLU Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain C1 residue 304 GLU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 60 LYS Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 212 ASN Chi-restraints excluded: chain D1 residue 299 GLU Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** 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 = 0.3504 r_free = 0.3504 target = 0.079896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065480 restraints weight = 38660.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067515 restraints weight = 23081.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068955 restraints weight = 16337.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069930 restraints weight = 12818.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070664 restraints weight = 10754.206| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11406 Z= 0.145 Angle : 0.593 9.389 15366 Z= 0.306 Chirality : 0.044 0.198 1694 Planarity : 0.004 0.036 1960 Dihedral : 4.056 19.540 1466 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.33 % Allowed : 18.68 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1368 helix: 0.37 (0.23), residues: 526 sheet: -0.71 (0.31), residues: 284 loop : -0.64 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGD1 329 TYR 0.025 0.002 TYRC1 217 PHE 0.048 0.002 PHE B 400 TRP 0.032 0.002 TRP A 296 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00332 (11406) covalent geometry : angle 0.59296 (15366) hydrogen bonds : bond 0.02985 ( 497) hydrogen bonds : angle 4.85876 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.572 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: A 370 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 523 ASP cc_start: 0.8249 (t0) cc_final: 0.7979 (t0) REVERT: A 585 MET cc_start: 0.8060 (tmm) cc_final: 0.7447 (tmm) REVERT: A 599 MET cc_start: 0.6089 (tpt) cc_final: 0.5643 (ppp) REVERT: B 385 MET cc_start: 0.8478 (tmm) cc_final: 0.8018 (tmm) REVERT: B 523 ASP cc_start: 0.8130 (t0) cc_final: 0.7236 (p0) REVERT: B 599 MET cc_start: 0.6013 (tpp) cc_final: 0.5129 (tmm) REVERT: B 644 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7820 (mp0) REVERT: C1 331 ASN cc_start: 0.8837 (m110) cc_final: 0.8591 (m110) REVERT: D1 60 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7664 (mttp) REVERT: D1 271 GLU cc_start: 0.8303 (tt0) cc_final: 0.7794 (tt0) REVERT: D1 299 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: D1 308 PHE cc_start: 0.8318 (m-10) cc_final: 0.7973 (m-10) REVERT: D1 331 ASN cc_start: 0.8737 (m110) cc_final: 0.8419 (m110) outliers start: 29 outliers final: 22 residues processed: 156 average time/residue: 0.1116 time to fit residues: 25.0678 Evaluate side-chains 149 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 97 GLU Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 60 LYS Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 298 ILE Chi-restraints excluded: chain D1 residue 299 GLU Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 97 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 GLN C1 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066977 restraints weight = 38560.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069041 restraints weight = 23564.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070442 restraints weight = 16910.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.071376 restraints weight = 13412.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072120 restraints weight = 11380.015| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11406 Z= 0.124 Angle : 0.590 9.750 15366 Z= 0.304 Chirality : 0.044 0.195 1694 Planarity : 0.004 0.036 1960 Dihedral : 4.027 19.355 1466 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.33 % Allowed : 19.08 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1368 helix: 0.37 (0.23), residues: 528 sheet: -0.69 (0.31), residues: 284 loop : -0.54 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGD1 329 TYR 0.015 0.001 TYRD1 23 PHE 0.043 0.001 PHE B 400 TRP 0.031 0.002 TRP A 296 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00283 (11406) covalent geometry : angle 0.58966 (15366) hydrogen bonds : bond 0.02943 ( 497) hydrogen bonds : angle 4.81646 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.467 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: A 370 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 578 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6374 (tt0) REVERT: A 585 MET cc_start: 0.8155 (tmm) cc_final: 0.7707 (tmm) REVERT: A 599 MET cc_start: 0.6062 (tpt) cc_final: 0.5655 (ppp) REVERT: B 523 ASP cc_start: 0.8014 (t0) cc_final: 0.7763 (t0) REVERT: B 599 MET cc_start: 0.5800 (tpp) cc_final: 0.4999 (tmm) REVERT: B 644 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7691 (mp0) REVERT: C1 262 GLU cc_start: 0.8106 (tt0) cc_final: 0.7793 (tt0) REVERT: C1 331 ASN cc_start: 0.8731 (m110) cc_final: 0.8518 (m110) REVERT: D1 271 GLU cc_start: 0.8221 (tt0) cc_final: 0.7708 (tt0) REVERT: D1 308 PHE cc_start: 0.8240 (m-10) cc_final: 0.7862 (m-10) REVERT: D1 329 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8025 (mtm-85) REVERT: D1 331 ASN cc_start: 0.8623 (m110) cc_final: 0.8311 (m110) outliers start: 29 outliers final: 20 residues processed: 163 average time/residue: 0.1122 time to fit residues: 26.2841 Evaluate side-chains 145 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 298 ILE Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 295 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 = 0.3552 r_free = 0.3552 target = 0.081461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067265 restraints weight = 38073.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069298 restraints weight = 23415.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070696 restraints weight = 16835.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071683 restraints weight = 13340.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072331 restraints weight = 11295.889| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11406 Z= 0.121 Angle : 0.610 12.395 15366 Z= 0.313 Chirality : 0.044 0.190 1694 Planarity : 0.004 0.036 1960 Dihedral : 4.065 21.785 1466 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.01 % Allowed : 19.57 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1368 helix: 0.41 (0.23), residues: 528 sheet: -0.70 (0.32), residues: 284 loop : -0.52 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGD1 329 TYR 0.020 0.001 TYRD1 23 PHE 0.040 0.001 PHE B 400 TRP 0.038 0.002 TRP A 296 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00277 (11406) covalent geometry : angle 0.60986 (15366) hydrogen bonds : bond 0.03057 ( 497) hydrogen bonds : angle 4.82883 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.416 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: A 370 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 585 MET cc_start: 0.8352 (tmm) cc_final: 0.7874 (tmm) REVERT: A 599 MET cc_start: 0.5993 (tpt) cc_final: 0.5644 (ppp) REVERT: B 385 MET cc_start: 0.8382 (tmm) cc_final: 0.7994 (tmm) REVERT: B 523 ASP cc_start: 0.8013 (t0) cc_final: 0.7737 (t0) REVERT: B 599 MET cc_start: 0.5966 (tpp) cc_final: 0.5188 (tmm) REVERT: B 644 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7760 (mp0) REVERT: C1 331 ASN cc_start: 0.8724 (m110) cc_final: 0.8503 (m110) REVERT: C1 338 ARG cc_start: 0.8298 (mtm110) cc_final: 0.8081 (mtp-110) REVERT: D1 271 GLU cc_start: 0.8216 (tt0) cc_final: 0.7706 (tt0) REVERT: D1 308 PHE cc_start: 0.8235 (m-10) cc_final: 0.7819 (m-10) REVERT: D1 331 ASN cc_start: 0.8628 (m110) cc_final: 0.8345 (m110) outliers start: 25 outliers final: 21 residues processed: 155 average time/residue: 0.1087 time to fit residues: 24.7295 Evaluate side-chains 148 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 298 ILE Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN A 592 GLN C1 247 GLN ** C1 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.065387 restraints weight = 39024.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067404 restraints weight = 24146.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068786 restraints weight = 17499.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069760 restraints weight = 14001.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070464 restraints weight = 11907.026| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11406 Z= 0.165 Angle : 0.631 10.668 15366 Z= 0.329 Chirality : 0.045 0.197 1694 Planarity : 0.004 0.035 1960 Dihedral : 4.186 21.750 1466 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.85 % Allowed : 20.29 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1368 helix: 0.39 (0.23), residues: 528 sheet: -0.73 (0.32), residues: 280 loop : -0.53 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGD1 329 TYR 0.021 0.002 TYRC1 23 PHE 0.047 0.002 PHE B 400 TRP 0.037 0.003 TRP A 296 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00374 (11406) covalent geometry : angle 0.63121 (15366) hydrogen bonds : bond 0.03183 ( 497) hydrogen bonds : angle 4.99687 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.382 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: A 370 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 585 MET cc_start: 0.8391 (tmm) cc_final: 0.7389 (tpp) REVERT: A 599 MET cc_start: 0.6070 (tpt) cc_final: 0.5548 (ppp) REVERT: A 602 TYR cc_start: 0.7618 (p90) cc_final: 0.7014 (p90) REVERT: B 326 ASP cc_start: 0.6271 (t0) cc_final: 0.6014 (t0) REVERT: B 385 MET cc_start: 0.8396 (tmm) cc_final: 0.8000 (tmm) REVERT: B 523 ASP cc_start: 0.8075 (t0) cc_final: 0.7803 (t0) REVERT: B 599 MET cc_start: 0.6205 (tpp) cc_final: 0.5408 (tmm) REVERT: B 603 MET cc_start: 0.5973 (ptm) cc_final: 0.5656 (ttp) REVERT: B 644 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7808 (mp0) REVERT: C1 331 ASN cc_start: 0.8732 (m110) cc_final: 0.8510 (m110) REVERT: D1 271 GLU cc_start: 0.8266 (tt0) cc_final: 0.7760 (tt0) REVERT: D1 308 PHE cc_start: 0.8312 (m-10) cc_final: 0.8039 (m-10) REVERT: D1 329 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8022 (mtm-85) REVERT: D1 331 ASN cc_start: 0.8606 (m110) cc_final: 0.8317 (m110) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.1072 time to fit residues: 22.6890 Evaluate side-chains 143 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 298 ILE Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN C1 152 ASN C1 212 ASN ** C1 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066012 restraints weight = 38749.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068051 restraints weight = 23898.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069452 restraints weight = 17290.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070424 restraints weight = 13811.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071114 restraints weight = 11739.542| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11406 Z= 0.135 Angle : 0.628 9.557 15366 Z= 0.326 Chirality : 0.045 0.191 1694 Planarity : 0.004 0.035 1960 Dihedral : 4.195 21.434 1466 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 21.10 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1368 helix: 0.37 (0.23), residues: 526 sheet: -0.74 (0.32), residues: 280 loop : -0.52 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGD1 329 TYR 0.020 0.001 TYRC1 23 PHE 0.048 0.002 PHE B 400 TRP 0.045 0.003 TRPD1 11 HIS 0.007 0.001 HISD1 309 Details of bonding type rmsd covalent geometry : bond 0.00306 (11406) covalent geometry : angle 0.62823 (15366) hydrogen bonds : bond 0.03155 ( 497) hydrogen bonds : angle 5.00835 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.71 seconds wall clock time: 30 minutes 28.66 seconds (1828.66 seconds total)