Starting phenix.real_space_refine on Tue Jul 29 10:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlb_22238/07_2025/6xlb_22238.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlb_22238/07_2025/6xlb_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_22238/07_2025/6xlb_22238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlb_22238/07_2025/6xlb_22238.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlb_22238/07_2025/6xlb_22238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlb_22238/07_2025/6xlb_22238.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.05, per 1000 atoms: 0.63 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.56 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: 3.56 Time building geometry restraints manager: 2.89 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: 0.03 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.710 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- 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 : 7.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.001 TRPC1 242 HIS 0.004 0.000 HIS A 304 PHE 0.008 0.001 PHE B 579 TYR 0.005 0.001 TYR A 469 ARG 0.001 0.000 ARGC1 329 Details of bonding type rmsd hydrogen bonds : bond 0.15424 ( 497) hydrogen bonds : angle 6.20015 ( 1404) covalent geometry : bond 0.00150 (11406) covalent geometry : angle 0.42784 (15366) *********************** 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 : 1.364 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: 0.7777 (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: 0.3081 time to fit residues: 143.2415 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 : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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 ** C1 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.084392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070091 restraints weight = 37552.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072220 restraints weight = 22174.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073737 restraints weight = 15500.363| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11406 Z= 0.164 Angle : 0.606 8.347 15366 Z= 0.317 Chirality : 0.045 0.186 1694 Planarity : 0.004 0.046 1960 Dihedral : 3.718 15.972 1466 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.85 % Allowed : 12.24 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1368 helix: -0.16 (0.22), residues: 522 sheet: -1.15 (0.30), residues: 278 loop : -1.07 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 296 HIS 0.011 0.002 HISD1 309 PHE 0.025 0.002 PHE A 288 TYR 0.023 0.002 TYRD1 335 ARG 0.006 0.001 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 497) hydrogen bonds : angle 5.11976 ( 1404) covalent geometry : bond 0.00368 (11406) covalent geometry : angle 0.60584 (15366) *********************** 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 229 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 1.331 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 396 LEU cc_start: 0.9747 (mt) cc_final: 0.9509 (mm) REVERT: A 460 MET cc_start: 0.7954 (mmm) cc_final: 0.7611 (mmm) REVERT: A 523 ASP cc_start: 0.8308 (t0) cc_final: 0.8064 (t0) REVERT: A 585 MET cc_start: 0.6751 (ttt) cc_final: 0.6437 (ttt) REVERT: A 599 MET cc_start: 0.5857 (tpt) cc_final: 0.5359 (ppp) REVERT: A 603 MET cc_start: 0.6199 (pmm) cc_final: 0.5045 (tpp) REVERT: B 362 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8127 (mtpt) REVERT: B 370 LEU cc_start: 0.7199 (tp) cc_final: 0.6997 (tt) REVERT: B 385 MET cc_start: 0.8571 (tmm) cc_final: 0.8285 (tmm) REVERT: B 574 ILE cc_start: 0.8972 (mm) cc_final: 0.8740 (mm) REVERT: B 599 MET cc_start: 0.5748 (tpp) cc_final: 0.4816 (tmm) REVERT: B 640 ASN cc_start: 0.8587 (t0) cc_final: 0.7554 (t0) REVERT: B 641 LEU cc_start: 0.9656 (tp) cc_final: 0.8939 (tt) REVERT: B 644 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7455 (mp0) REVERT: C1 25 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8362 (mttm) REVERT: C1 217 TYR cc_start: 0.9023 (t80) cc_final: 0.7787 (t80) REVERT: C1 231 GLU cc_start: 0.8216 (mp0) cc_final: 0.7917 (mp0) REVERT: C1 314 GLN cc_start: 0.8742 (tt0) cc_final: 0.8422 (tt0) REVERT: C1 317 TRP cc_start: 0.8687 (t60) cc_final: 0.8335 (t60) REVERT: C1 331 ASN cc_start: 0.8676 (m110) cc_final: 0.8452 (m110) REVERT: C1 335 TYR cc_start: 0.8147 (m-80) cc_final: 0.7698 (m-10) REVERT: D1 271 GLU cc_start: 0.8166 (tt0) cc_final: 0.7548 (tt0) REVERT: D1 331 ASN cc_start: 0.8796 (m110) cc_final: 0.8581 (m-40) outliers start: 23 outliers final: 12 residues processed: 215 average time/residue: 0.3574 time to fit residues: 106.0597 Evaluate side-chains 174 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 212 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 336 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067749 restraints weight = 38419.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069876 restraints weight = 22968.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071346 restraints weight = 16235.446| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11406 Z= 0.156 Angle : 0.594 9.678 15366 Z= 0.309 Chirality : 0.045 0.166 1694 Planarity : 0.004 0.044 1960 Dihedral : 3.923 17.220 1466 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 14.81 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1368 helix: 0.04 (0.23), residues: 526 sheet: -1.02 (0.30), residues: 278 loop : -0.87 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 296 HIS 0.016 0.002 HISD1 309 PHE 0.036 0.002 PHE B 400 TYR 0.016 0.002 TYRD1 335 ARG 0.006 0.001 ARGC1 329 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 497) hydrogen bonds : angle 4.98469 ( 1404) covalent geometry : bond 0.00350 (11406) covalent geometry : angle 0.59363 (15366) *********************** 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 209 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.405 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 385 MET cc_start: 0.8383 (tmm) cc_final: 0.8079 (tmm) REVERT: A 502 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: A 523 ASP cc_start: 0.8326 (t0) cc_final: 0.8072 (t0) REVERT: A 599 MET cc_start: 0.6108 (tpt) cc_final: 0.5530 (ppp) REVERT: B 370 LEU cc_start: 0.7367 (tp) cc_final: 0.7150 (tt) REVERT: B 385 MET cc_start: 0.8605 (tmm) cc_final: 0.8314 (tmm) REVERT: B 589 MET cc_start: 0.7236 (mtp) cc_final: 0.5044 (mtp) REVERT: B 599 MET cc_start: 0.5720 (tpp) cc_final: 0.4788 (tmm) REVERT: B 640 ASN cc_start: 0.8733 (t0) cc_final: 0.7432 (t0) REVERT: B 641 LEU cc_start: 0.9581 (tp) cc_final: 0.8892 (tt) REVERT: B 644 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7413 (mp0) REVERT: C1 25 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8322 (mttm) REVERT: C1 94 ASN cc_start: 0.8826 (p0) cc_final: 0.8524 (p0) REVERT: C1 231 GLU cc_start: 0.8300 (mp0) cc_final: 0.7964 (mp0) REVERT: C1 271 GLU cc_start: 0.7086 (tp30) cc_final: 0.6593 (tp30) REVERT: C1 314 GLN cc_start: 0.8853 (tt0) cc_final: 0.8579 (tt0) REVERT: C1 317 TRP cc_start: 0.8770 (t60) cc_final: 0.8513 (t60) REVERT: C1 331 ASN cc_start: 0.8776 (m110) cc_final: 0.8507 (m110) REVERT: D1 271 GLU cc_start: 0.8174 (tt0) cc_final: 0.7547 (tt0) REVERT: D1 314 GLN cc_start: 0.8958 (pt0) cc_final: 0.8575 (pt0) REVERT: D1 331 ASN cc_start: 0.8779 (m110) cc_final: 0.8512 (m110) outliers start: 25 outliers final: 14 residues processed: 198 average time/residue: 0.2870 time to fit residues: 80.2227 Evaluate side-chains 159 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 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 667 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 93 ILE Chi-restraints excluded: chain D1 residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 58 GLN ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 314 GLN D1 250 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068239 restraints weight = 38126.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070292 restraints weight = 23287.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071729 restraints weight = 16661.879| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3727 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= 0.117 Angle : 0.559 8.446 15366 Z= 0.290 Chirality : 0.044 0.219 1694 Planarity : 0.004 0.041 1960 Dihedral : 4.005 20.035 1466 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.06 % Allowed : 15.78 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1368 helix: 0.17 (0.23), residues: 526 sheet: -0.91 (0.29), residues: 298 loop : -0.77 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 296 HIS 0.008 0.001 HIS A 304 PHE 0.027 0.001 PHE B 400 TYR 0.021 0.002 TYRC1 335 ARG 0.006 0.001 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 497) hydrogen bonds : angle 4.87110 ( 1404) covalent geometry : bond 0.00264 (11406) covalent geometry : angle 0.55914 (15366) *********************** 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 206 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.218 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: A 502 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: A 523 ASP cc_start: 0.8288 (t0) cc_final: 0.8007 (t0) REVERT: A 599 MET cc_start: 0.6065 (tpt) cc_final: 0.5547 (ppp) REVERT: B 370 LEU cc_start: 0.7352 (tp) cc_final: 0.7122 (tt) REVERT: B 385 MET cc_start: 0.8551 (tmm) cc_final: 0.8275 (tmm) REVERT: B 599 MET cc_start: 0.5739 (tpp) cc_final: 0.4821 (tmm) REVERT: B 640 ASN cc_start: 0.8548 (t0) cc_final: 0.6957 (t0) REVERT: B 641 LEU cc_start: 0.9530 (tp) cc_final: 0.8847 (tt) REVERT: B 644 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7361 (mp0) REVERT: C1 94 ASN cc_start: 0.8745 (p0) cc_final: 0.8433 (p0) REVERT: C1 231 GLU cc_start: 0.8224 (mp0) cc_final: 0.7864 (mp0) REVERT: C1 331 ASN cc_start: 0.8745 (m110) cc_final: 0.8477 (m110) REVERT: C1 346 PHE cc_start: 0.8602 (m-10) cc_final: 0.8270 (m-80) REVERT: D1 271 GLU cc_start: 0.8065 (tt0) cc_final: 0.7436 (tt0) REVERT: D1 308 PHE cc_start: 0.8306 (m-10) cc_final: 0.8069 (m-10) REVERT: D1 314 GLN cc_start: 0.8920 (pt0) cc_final: 0.8392 (pt0) REVERT: D1 331 ASN cc_start: 0.8797 (m110) cc_final: 0.8532 (m110) outliers start: 38 outliers final: 23 residues processed: 194 average time/residue: 0.2223 time to fit residues: 61.9850 Evaluate side-chains 169 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 365 VAL 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 634 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 141 GLN Chi-restraints excluded: chain C1 residue 304 GLU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 93 ILE Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 257 THR Chi-restraints excluded: chain D1 residue 315 VAL 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 84 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C1 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.079224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064715 restraints weight = 38984.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066665 restraints weight = 24096.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068035 restraints weight = 17511.008| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11406 Z= 0.220 Angle : 0.629 8.981 15366 Z= 0.330 Chirality : 0.045 0.157 1694 Planarity : 0.004 0.041 1960 Dihedral : 4.284 20.749 1466 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.66 % Allowed : 17.39 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1368 helix: 0.33 (0.23), residues: 528 sheet: -0.87 (0.29), residues: 300 loop : -0.69 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 296 HIS 0.005 0.001 HISC1 284 PHE 0.039 0.002 PHE B 400 TYR 0.016 0.002 TYRD1 23 ARG 0.005 0.001 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 497) hydrogen bonds : angle 5.05427 ( 1404) covalent geometry : bond 0.00484 (11406) covalent geometry : angle 0.62887 (15366) *********************** 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: 33 poor density : 142 time to evaluate : 1.273 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: 0.8220 (t0) cc_final: 0.7969 (t0) REVERT: A 599 MET cc_start: 0.6159 (tpt) cc_final: 0.5738 (ppp) REVERT: B 370 LEU cc_start: 0.7516 (tp) cc_final: 0.7244 (tt) REVERT: B 385 MET cc_start: 0.8558 (tmm) cc_final: 0.8216 (tmm) REVERT: B 396 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9573 (tt) REVERT: B 523 ASP cc_start: 0.8027 (t0) cc_final: 0.7789 (t0) REVERT: B 595 ARG cc_start: 0.6693 (tmt170) cc_final: 0.5727 (tmt170) REVERT: B 599 MET cc_start: 0.5991 (tpp) cc_final: 0.5075 (tmm) REVERT: B 640 ASN cc_start: 0.8528 (t0) cc_final: 0.7117 (t0) REVERT: B 644 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7202 (mp0) REVERT: B 648 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8835 (mm) REVERT: C1 32 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: C1 94 ASN cc_start: 0.8770 (p0) cc_final: 0.8540 (p0) REVERT: C1 231 GLU cc_start: 0.8262 (mp0) cc_final: 0.7989 (mp0) REVERT: C1 271 GLU cc_start: 0.7459 (tp30) cc_final: 0.7081 (tp30) REVERT: C1 312 LYS cc_start: 0.9124 (mtpp) cc_final: 0.8853 (mtpp) REVERT: C1 327 ARG cc_start: 0.8287 (ttt180) cc_final: 0.7951 (ttt180) REVERT: C1 331 ASN cc_start: 0.8723 (m110) cc_final: 0.8477 (m110) REVERT: D1 60 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7657 (mttp) REVERT: D1 271 GLU cc_start: 0.8327 (tt0) cc_final: 0.7779 (tt0) REVERT: D1 308 PHE cc_start: 0.8295 (m-10) cc_final: 0.7876 (m-10) REVERT: D1 331 ASN cc_start: 0.8743 (m110) cc_final: 0.8488 (m110) outliers start: 33 outliers final: 24 residues processed: 165 average time/residue: 0.2644 time to fit residues: 60.5802 Evaluate side-chains 154 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 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 361 VAL Chi-restraints excluded: chain B residue 365 VAL 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 554 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 32 GLU Chi-restraints excluded: chain C1 residue 95 VAL 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 66 LEU Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 93 ILE Chi-restraints excluded: chain D1 residue 257 THR 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 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 108 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7624 ------------------------------------------------------------------------------- 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 D1 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.081190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066524 restraints weight = 38806.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068559 restraints weight = 23929.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069995 restraints weight = 17300.377| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4554 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= 0.123 Angle : 0.582 9.373 15366 Z= 0.301 Chirality : 0.044 0.165 1694 Planarity : 0.004 0.057 1960 Dihedral : 4.172 21.735 1466 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.58 % Allowed : 18.20 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1368 helix: 0.26 (0.23), residues: 538 sheet: -0.68 (0.31), residues: 278 loop : -0.66 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 296 HIS 0.010 0.001 HISD1 309 PHE 0.039 0.001 PHE B 400 TYR 0.023 0.002 TYRC1 217 ARG 0.008 0.001 ARGD1 329 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 497) hydrogen bonds : angle 4.93998 ( 1404) covalent geometry : bond 0.00281 (11406) covalent geometry : angle 0.58212 (15366) *********************** 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 190 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.346 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 523 ASP cc_start: 0.8166 (t0) cc_final: 0.7891 (t0) REVERT: A 599 MET cc_start: 0.6068 (tpt) cc_final: 0.5671 (ppp) REVERT: B 370 LEU cc_start: 0.7388 (tp) cc_final: 0.7114 (tt) REVERT: B 385 MET cc_start: 0.8457 (tmm) cc_final: 0.8183 (tmm) REVERT: B 523 ASP cc_start: 0.8014 (t0) cc_final: 0.7271 (p0) REVERT: B 595 ARG cc_start: 0.5972 (tmt170) cc_final: 0.5728 (tmt170) REVERT: B 599 MET cc_start: 0.6119 (tpp) cc_final: 0.5147 (tmm) REVERT: B 640 ASN cc_start: 0.8529 (t0) cc_final: 0.7982 (t0) REVERT: B 648 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8828 (mm) REVERT: C1 32 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: C1 94 ASN cc_start: 0.8707 (p0) cc_final: 0.8460 (p0) REVERT: C1 231 GLU cc_start: 0.8085 (mp0) cc_final: 0.7632 (mp0) REVERT: C1 238 ARG cc_start: 0.8478 (mtm180) cc_final: 0.7852 (mtm180) REVERT: D1 212 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7646 (t0) REVERT: D1 271 GLU cc_start: 0.8151 (tt0) cc_final: 0.7593 (tt0) REVERT: D1 308 PHE cc_start: 0.8187 (m-10) cc_final: 0.7852 (m-10) REVERT: D1 312 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8068 (ttpp) REVERT: D1 331 ASN cc_start: 0.8562 (m110) cc_final: 0.8235 (m110) outliers start: 32 outliers final: 24 residues processed: 177 average time/residue: 0.2388 time to fit residues: 61.0977 Evaluate side-chains 159 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 361 VAL Chi-restraints excluded: chain B residue 365 VAL 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 602 TYR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 16 CYS Chi-restraints excluded: chain C1 residue 32 GLU Chi-restraints excluded: chain C1 residue 95 VAL 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 66 LEU Chi-restraints excluded: chain D1 residue 71 ILE Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 212 ASN 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 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 237 GLN D1 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066550 restraints weight = 38895.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068551 restraints weight = 24009.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069919 restraints weight = 17386.575| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11406 Z= 0.126 Angle : 0.585 9.410 15366 Z= 0.303 Chirality : 0.044 0.218 1694 Planarity : 0.004 0.045 1960 Dihedral : 4.140 21.005 1466 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.74 % Allowed : 18.92 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1368 helix: 0.30 (0.23), residues: 538 sheet: -0.67 (0.32), residues: 282 loop : -0.67 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 296 HIS 0.007 0.001 HIS A 304 PHE 0.036 0.002 PHE B 400 TYR 0.021 0.002 TYRD1 23 ARG 0.007 0.001 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 497) hydrogen bonds : angle 4.93024 ( 1404) covalent geometry : bond 0.00287 (11406) covalent geometry : angle 0.58475 (15366) *********************** 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 180 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.217 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 385 MET cc_start: 0.8373 (tmm) cc_final: 0.8013 (tmm) REVERT: A 578 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6434 (tt0) REVERT: A 599 MET cc_start: 0.6065 (tpt) cc_final: 0.5680 (ppp) REVERT: B 370 LEU cc_start: 0.7410 (tp) cc_final: 0.7135 (tt) REVERT: B 523 ASP cc_start: 0.8051 (t0) cc_final: 0.7273 (p0) REVERT: B 599 MET cc_start: 0.6131 (tpp) cc_final: 0.5191 (tmm) REVERT: B 640 ASN cc_start: 0.8554 (t0) cc_final: 0.8001 (t0) REVERT: B 648 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8846 (mm) REVERT: C1 70 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7920 (tptt) REVERT: C1 94 ASN cc_start: 0.8685 (p0) cc_final: 0.8264 (p0) REVERT: C1 231 GLU cc_start: 0.8078 (mp0) cc_final: 0.7721 (mp0) REVERT: C1 238 ARG cc_start: 0.8427 (mtm180) cc_final: 0.7949 (mtm180) REVERT: C1 312 LYS cc_start: 0.9183 (mtpp) cc_final: 0.8856 (mtpp) REVERT: D1 271 GLU cc_start: 0.8126 (tt0) cc_final: 0.7527 (tt0) REVERT: D1 308 PHE cc_start: 0.8313 (m-10) cc_final: 0.7989 (m-10) REVERT: D1 312 LYS cc_start: 0.8296 (ttpp) cc_final: 0.7983 (ttpp) REVERT: D1 331 ASN cc_start: 0.8551 (m110) cc_final: 0.8229 (m110) outliers start: 34 outliers final: 20 residues processed: 170 average time/residue: 0.2404 time to fit residues: 58.4056 Evaluate side-chains 157 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 365 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 667 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 287 LEU Chi-restraints excluded: chain C1 residue 349 VAL Chi-restraints excluded: chain D1 residue 93 ILE Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 257 THR 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 3 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 chunk 92 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN C1 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067195 restraints weight = 38719.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069227 restraints weight = 23877.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070644 restraints weight = 17278.109| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4799 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= 0.115 Angle : 0.591 9.554 15366 Z= 0.304 Chirality : 0.044 0.173 1694 Planarity : 0.004 0.042 1960 Dihedral : 4.113 20.359 1466 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 19.97 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1368 helix: 0.27 (0.23), residues: 542 sheet: -0.66 (0.32), residues: 282 loop : -0.58 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 296 HIS 0.007 0.001 HIS A 304 PHE 0.053 0.002 PHE B 400 TYR 0.023 0.002 TYRC1 217 ARG 0.008 0.001 ARGD1 329 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 497) hydrogen bonds : angle 4.92001 ( 1404) covalent geometry : bond 0.00258 (11406) covalent geometry : angle 0.59121 (15366) *********************** 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 186 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.253 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: A 378 MET cc_start: 0.3438 (tmm) cc_final: 0.3020 (tmm) REVERT: A 578 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6089 (tt0) REVERT: A 599 MET cc_start: 0.6237 (tpt) cc_final: 0.5593 (ppp) REVERT: A 602 TYR cc_start: 0.7638 (p90) cc_final: 0.7077 (p90) REVERT: B 370 LEU cc_start: 0.7459 (tp) cc_final: 0.7187 (tt) REVERT: B 385 MET cc_start: 0.8513 (tmm) cc_final: 0.8012 (tmm) REVERT: B 396 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9556 (tt) REVERT: B 523 ASP cc_start: 0.8017 (t0) cc_final: 0.7261 (p0) REVERT: B 595 ARG cc_start: 0.6683 (tmt170) cc_final: 0.5843 (tmm-80) REVERT: B 599 MET cc_start: 0.6097 (tpp) cc_final: 0.5175 (tmm) REVERT: B 640 ASN cc_start: 0.8536 (t0) cc_final: 0.7984 (t0) REVERT: B 648 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C1 70 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8094 (tptt) REVERT: C1 94 ASN cc_start: 0.8654 (p0) cc_final: 0.8241 (p0) REVERT: C1 128 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8128 (mtm-85) REVERT: C1 231 GLU cc_start: 0.8038 (mp0) cc_final: 0.7806 (mp0) REVERT: C1 312 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8891 (mtpp) REVERT: D1 271 GLU cc_start: 0.8051 (tt0) cc_final: 0.7284 (tt0) REVERT: D1 284 HIS cc_start: 0.8516 (m-70) cc_final: 0.8154 (m90) REVERT: D1 308 PHE cc_start: 0.8338 (m-10) cc_final: 0.7977 (m-10) REVERT: D1 312 LYS cc_start: 0.8282 (ttpp) cc_final: 0.7939 (ttpp) REVERT: D1 329 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8069 (mtm-85) REVERT: D1 331 ASN cc_start: 0.8509 (m110) cc_final: 0.8210 (m110) outliers start: 23 outliers final: 16 residues processed: 178 average time/residue: 0.2455 time to fit residues: 62.2655 Evaluate side-chains 162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 594 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 70 LYS Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain D1 residue 93 ILE Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 315 VAL Chi-restraints excluded: chain D1 residue 317 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 67 optimal weight: 0.0050 chunk 81 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 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 = 0.3548 r_free = 0.3548 target = 0.081478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067146 restraints weight = 38805.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069146 restraints weight = 24327.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070498 restraints weight = 17704.579| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11406 Z= 0.119 Angle : 0.600 9.663 15366 Z= 0.308 Chirality : 0.044 0.191 1694 Planarity : 0.004 0.042 1960 Dihedral : 4.095 21.055 1466 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.85 % Allowed : 19.97 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1368 helix: 0.30 (0.23), residues: 544 sheet: -0.67 (0.32), residues: 282 loop : -0.54 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 296 HIS 0.006 0.001 HIS A 304 PHE 0.051 0.002 PHE B 400 TYR 0.021 0.001 TYRD1 23 ARG 0.008 0.001 ARGD1 329 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 497) hydrogen bonds : angle 4.93041 ( 1404) covalent geometry : bond 0.00272 (11406) covalent geometry : angle 0.60038 (15366) *********************** 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 177 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.369 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 378 MET cc_start: 0.3620 (tmm) cc_final: 0.3202 (tmm) REVERT: A 578 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6246 (tt0) REVERT: A 599 MET cc_start: 0.6211 (tpt) cc_final: 0.5571 (ppp) REVERT: A 602 TYR cc_start: 0.7766 (p90) cc_final: 0.7163 (p90) REVERT: B 370 LEU cc_start: 0.7600 (tp) cc_final: 0.7326 (tt) REVERT: B 385 MET cc_start: 0.8563 (tmm) cc_final: 0.8214 (tmm) REVERT: B 396 LEU cc_start: 0.9785 (OUTLIER) cc_final: 0.9564 (tt) REVERT: B 523 ASP cc_start: 0.8027 (t0) cc_final: 0.7227 (p0) REVERT: B 595 ARG cc_start: 0.6826 (tmt170) cc_final: 0.5887 (tmm-80) REVERT: B 599 MET cc_start: 0.6235 (tpp) cc_final: 0.5301 (tmm) REVERT: B 640 ASN cc_start: 0.8563 (t0) cc_final: 0.8018 (t0) REVERT: B 648 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C1 312 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8897 (mtpp) REVERT: D1 271 GLU cc_start: 0.8104 (tt0) cc_final: 0.7375 (tt0) REVERT: D1 284 HIS cc_start: 0.8539 (m-70) cc_final: 0.8210 (m90) REVERT: D1 308 PHE cc_start: 0.8352 (m-10) cc_final: 0.7970 (m-10) REVERT: D1 312 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8045 (ttpp) REVERT: D1 329 ARG cc_start: 0.8349 (ttm110) cc_final: 0.8050 (mtm-85) REVERT: D1 331 ASN cc_start: 0.8471 (m110) cc_final: 0.8197 (m110) outliers start: 23 outliers final: 17 residues processed: 169 average time/residue: 0.2424 time to fit residues: 58.4868 Evaluate side-chains 158 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU 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 365 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C1 residue 95 VAL Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain D1 residue 93 ILE Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 257 THR Chi-restraints excluded: chain D1 residue 315 VAL Chi-restraints excluded: chain D1 residue 317 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 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 = 0.3534 r_free = 0.3534 target = 0.080938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066718 restraints weight = 38774.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068685 restraints weight = 24406.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070034 restraints weight = 17850.941| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5098 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= 0.132 Angle : 0.602 9.671 15366 Z= 0.311 Chirality : 0.045 0.196 1694 Planarity : 0.004 0.044 1960 Dihedral : 4.125 20.812 1466 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.77 % Allowed : 20.13 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1368 helix: 0.30 (0.23), residues: 544 sheet: -0.70 (0.32), residues: 282 loop : -0.54 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 273 HIS 0.006 0.001 HIS A 304 PHE 0.052 0.002 PHE B 400 TYR 0.026 0.002 TYRC1 23 ARG 0.007 0.001 ARGD1 329 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 497) hydrogen bonds : angle 4.96567 ( 1404) covalent geometry : bond 0.00303 (11406) covalent geometry : angle 0.60166 (15366) ********************** 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 164 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.258 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: A 385 MET cc_start: 0.8560 (tmm) cc_final: 0.8238 (tmm) REVERT: A 578 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6282 (tt0) REVERT: A 599 MET cc_start: 0.6221 (tpt) cc_final: 0.5618 (ppp) REVERT: A 602 TYR cc_start: 0.7738 (p90) cc_final: 0.7117 (p90) REVERT: A 666 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: B 326 ASP cc_start: 0.6275 (t0) cc_final: 0.6015 (t0) REVERT: B 370 LEU cc_start: 0.7551 (tp) cc_final: 0.7266 (tt) REVERT: B 385 MET cc_start: 0.8555 (tmm) cc_final: 0.8199 (tmm) REVERT: B 396 LEU cc_start: 0.9789 (mt) cc_final: 0.9569 (tt) REVERT: B 523 ASP cc_start: 0.7997 (t0) cc_final: 0.7234 (p0) REVERT: B 546 LEU cc_start: 0.9235 (tp) cc_final: 0.8994 (mt) REVERT: B 599 MET cc_start: 0.6277 (tpp) cc_final: 0.5362 (tmm) REVERT: B 640 ASN cc_start: 0.8646 (t0) cc_final: 0.7346 (t0) REVERT: B 644 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7399 (mp0) REVERT: B 648 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8815 (mm) REVERT: C1 128 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: C1 312 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8871 (mtpp) REVERT: D1 271 GLU cc_start: 0.8170 (tt0) cc_final: 0.7427 (tt0) REVERT: D1 284 HIS cc_start: 0.8538 (m-70) cc_final: 0.8181 (m90) REVERT: D1 308 PHE cc_start: 0.8393 (m-10) cc_final: 0.8090 (m-10) REVERT: D1 309 HIS cc_start: 0.7610 (p-80) cc_final: 0.7372 (p-80) REVERT: D1 312 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8014 (ttpp) REVERT: D1 329 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8068 (mtm-85) REVERT: D1 331 ASN cc_start: 0.8463 (m110) cc_final: 0.8194 (m110) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 0.2581 time to fit residues: 56.4877 Evaluate side-chains 157 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU 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 641 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain C1 residue 111 ILE Chi-restraints excluded: chain C1 residue 287 LEU Chi-restraints excluded: chain D1 residue 141 GLN Chi-restraints excluded: chain D1 residue 257 THR Chi-restraints excluded: chain D1 residue 315 VAL Chi-restraints excluded: chain D1 residue 317 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.081187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066917 restraints weight = 38588.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068892 restraints weight = 24174.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070257 restraints weight = 17619.126| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5212 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= 0.123 Angle : 0.595 9.755 15366 Z= 0.307 Chirality : 0.044 0.184 1694 Planarity : 0.004 0.045 1960 Dihedral : 4.113 21.723 1466 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.37 % Allowed : 20.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1368 helix: 0.34 (0.23), residues: 544 sheet: -0.71 (0.32), residues: 278 loop : -0.52 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPD1 11 HIS 0.006 0.001 HIS A 304 PHE 0.050 0.002 PHE B 400 TYR 0.027 0.001 TYRC1 23 ARG 0.007 0.001 ARGD1 329 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 497) hydrogen bonds : angle 4.94296 ( 1404) covalent geometry : bond 0.00281 (11406) covalent geometry : angle 0.59525 (15366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3376.78 seconds wall clock time: 60 minutes 21.25 seconds (3621.25 seconds total)