Starting phenix.real_space_refine on Wed Jun 3 12:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r8p_53835/06_2026/9r8p_53835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r8p_53835/06_2026/9r8p_53835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r8p_53835/06_2026/9r8p_53835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r8p_53835/06_2026/9r8p_53835.map" model { file = "/net/cci-nas-00/data/ceres_data/9r8p_53835/06_2026/9r8p_53835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r8p_53835/06_2026/9r8p_53835.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 43 5.16 5 C 2980 2.51 5 N 795 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4714 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4714 Classifications: {'peptide': 582} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 556} Time building chain proxies: 1.21, per 1000 atoms: 0.26 Number of scatterers: 4714 At special positions: 0 Unit cell: (70.224, 103.664, 100.32, 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 43 16.00 O 896 8.00 N 795 7.00 C 2980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 127.7 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 67.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.877A pdb=" N ARG A 10 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 30 removed outlier: 3.883A pdb=" N LYS A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.916A pdb=" N LYS A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.748A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 70' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.805A pdb=" N ASP A 89 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS A 90 " --> pdb=" O MET A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.781A pdb=" N LEU A 103 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.827A pdb=" N PHE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.982A pdb=" N TYR A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 178 through 206 removed outlier: 3.882A pdb=" N ASP A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 204 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.141A pdb=" N TRP A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.895A pdb=" N GLU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 246 " --> pdb=" O HIS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.787A pdb=" N MET A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.500A pdb=" N CYS A 278 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 279' Processing helix chain 'A' and resid 282 through 291 removed outlier: 4.527A pdb=" N SER A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.738A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 4.004A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 365 through 369 removed outlier: 4.349A pdb=" N GLU A 368 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.584A pdb=" N GLU A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 removed outlier: 4.109A pdb=" N GLN A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA A 406 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 removed outlier: 3.889A pdb=" N ASN A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 466 removed outlier: 3.922A pdb=" N ASP A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.803A pdb=" N THR A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 512 through 516 removed outlier: 4.105A pdb=" N THR A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 516' Processing helix chain 'A' and resid 522 through 536 removed outlier: 4.178A pdb=" N PHE A 528 " --> pdb=" O MET A 524 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 removed outlier: 3.703A pdb=" N ALA A 546 " --> pdb=" O GLN A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.754A pdb=" N PHE A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 583 removed outlier: 3.663A pdb=" N ALA A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN A 580 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 483 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: 0.57 Time building geometry restraints manager: 0.52 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: 1559 1.34 - 1.46: 972 1.46 - 1.58: 2225 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 4807 Sorted by residual: bond pdb=" N ASP A 269 " pdb=" CA ASP A 269 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.35e-02 5.49e+03 8.00e+00 bond pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.89e+00 bond pdb=" N GLN A 268 " pdb=" CA GLN A 268 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.63e+00 bond pdb=" CA SER A 270 " pdb=" CB SER A 270 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.69e-02 3.50e+03 5.23e+00 bond pdb=" N SER A 272 " pdb=" CA SER A 272 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.32e-02 5.74e+03 4.66e+00 ... (remaining 4802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 6201 1.02 - 2.05: 202 2.05 - 3.07: 51 3.07 - 4.10: 9 4.10 - 5.12: 6 Bond angle restraints: 6469 Sorted by residual: angle pdb=" N SER A 270 " pdb=" CA SER A 270 " pdb=" C SER A 270 " ideal model delta sigma weight residual 113.02 108.25 4.77 1.20e+00 6.94e-01 1.58e+01 angle pdb=" CA ILE A 271 " pdb=" C ILE A 271 " pdb=" O ILE A 271 " ideal model delta sigma weight residual 120.78 117.25 3.53 1.25e+00 6.40e-01 7.98e+00 angle pdb=" CA SER A 272 " pdb=" C SER A 272 " pdb=" O SER A 272 " ideal model delta sigma weight residual 121.36 118.43 2.93 1.06e+00 8.90e-01 7.63e+00 angle pdb=" N PHE A 309 " pdb=" CA PHE A 309 " pdb=" C PHE A 309 " ideal model delta sigma weight residual 114.62 111.73 2.89 1.14e+00 7.69e-01 6.41e+00 angle pdb=" CA MET A 250 " pdb=" C MET A 250 " pdb=" N LEU A 251 " ideal model delta sigma weight residual 119.71 116.92 2.79 1.17e+00 7.31e-01 5.69e+00 ... (remaining 6464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2805 17.94 - 35.87: 199 35.87 - 53.81: 37 53.81 - 71.74: 7 71.74 - 89.68: 3 Dihedral angle restraints: 3051 sinusoidal: 1308 harmonic: 1743 Sorted by residual: dihedral pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " pdb=" CD GLU A 277 " pdb=" OE1 GLU A 277 " ideal model delta sinusoidal sigma weight residual 0.00 89.68 -89.68 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 565 " pdb=" CG GLU A 565 " pdb=" CD GLU A 565 " pdb=" OE1 GLU A 565 " ideal model delta sinusoidal sigma weight residual 0.00 86.70 -86.70 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 400 " pdb=" CG GLU A 400 " pdb=" CD GLU A 400 " pdb=" OE1 GLU A 400 " ideal model delta sinusoidal sigma weight residual 0.00 -86.19 86.19 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 3048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 439 0.031 - 0.061: 221 0.061 - 0.092: 36 0.092 - 0.122: 8 0.122 - 0.153: 1 Chirality restraints: 705 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA VAL A 418 " pdb=" N VAL A 418 " pdb=" C VAL A 418 " pdb=" CB VAL A 418 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA VAL A 122 " pdb=" N VAL A 122 " pdb=" C VAL A 122 " pdb=" CB VAL A 122 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.52e-01 ... (remaining 702 not shown) Planarity restraints: 842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 415 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 416 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 146 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 147 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 117 " -0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 118 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.015 5.00e-02 4.00e+02 ... (remaining 839 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 890 2.77 - 3.30: 4517 3.30 - 3.83: 7074 3.83 - 4.37: 8227 4.37 - 4.90: 13823 Nonbonded interactions: 34531 Sorted by model distance: nonbonded pdb=" OE2 GLU A 208 " pdb=" OG1 THR A 239 " model vdw 2.231 3.040 nonbonded pdb=" O ILE A 216 " pdb=" OG SER A 220 " model vdw 2.276 3.040 nonbonded pdb=" O ALA A 226 " pdb=" OH TYR A 332 " model vdw 2.300 3.040 nonbonded pdb=" NZ LYS A 414 " pdb=" O PHE A 488 " model vdw 2.353 3.120 nonbonded pdb=" O GLU A 37 " pdb=" NZ LYS A 41 " model vdw 2.355 3.120 ... (remaining 34526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.003 0.039 4823 Z= 0.142 Angle : 0.497 5.122 6501 Z= 0.276 Chirality : 0.035 0.153 705 Planarity : 0.004 0.043 842 Dihedral : 12.424 89.675 1861 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.11 % Allowed : 9.60 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.31), residues: 580 helix: -2.92 (0.21), residues: 304 sheet: None (None), residues: 0 loop : -1.57 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.005 0.001 TYR A 411 PHE 0.008 0.001 PHE A 36 TRP 0.002 0.001 TRP A 214 HIS 0.001 0.000 HIS A 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 4807) covalent geometry : angle 0.49322 / 0.27 ( 6469) SS BOND : bond 0.00161 / 0.13 ( 16) SS BOND : angle 1.03109 / 0.90 ( 32) hydrogen bonds : bond 0.28604 / 19.52 ( 170) hydrogen bonds : angle 7.90829 / 5.12 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.119 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: A 488 PHE cc_start: 0.6929 (t80) cc_final: 0.6557 (t80) outliers start: 11 outliers final: 2 residues processed: 63 average time/residue: 0.0868 time to fit residues: 6.9103 Evaluate side-chains 33 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 418 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.051759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038020 restraints weight = 38203.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039263 restraints weight = 27532.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040209 restraints weight = 21667.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.040936 restraints weight = 17995.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041490 restraints weight = 15570.979| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4823 Z= 0.148 Angle : 0.604 6.318 6501 Z= 0.304 Chirality : 0.040 0.296 705 Planarity : 0.004 0.025 842 Dihedral : 3.396 17.358 629 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.54 % Allowed : 13.44 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.34), residues: 580 helix: -1.36 (0.28), residues: 309 sheet: None (None), residues: 0 loop : -1.26 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.006 0.001 TYR A 353 PHE 0.010 0.001 PHE A 36 TRP 0.008 0.002 TRP A 214 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 4807) covalent geometry : angle 0.60202 / 0.30 ( 6469) SS BOND : bond 0.00327 / 0.25 ( 16) SS BOND : angle 0.86635 / 0.68 ( 32) hydrogen bonds : bond 0.04927 / 3.27 ( 170) hydrogen bonds : angle 4.43837 / 2.88 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 PHE cc_start: 0.9740 (t80) cc_final: 0.9430 (m-80) REVERT: A 551 PHE cc_start: 0.9702 (t80) cc_final: 0.9011 (t80) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.0464 time to fit residues: 2.9512 Evaluate side-chains 34 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 533 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.052148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038559 restraints weight = 37920.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039812 restraints weight = 27428.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040757 restraints weight = 21607.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041470 restraints weight = 17947.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042026 restraints weight = 15543.204| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4823 Z= 0.096 Angle : 0.536 7.417 6501 Z= 0.259 Chirality : 0.039 0.193 705 Planarity : 0.003 0.029 842 Dihedral : 3.204 14.172 628 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.30 % Allowed : 12.86 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.35), residues: 580 helix: -0.85 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -1.04 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.006 0.001 TYR A 319 PHE 0.031 0.001 PHE A 395 TRP 0.006 0.002 TRP A 214 HIS 0.006 0.000 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 4807) covalent geometry : angle 0.53457 / 0.26 ( 6469) SS BOND : bond 0.00180 / 0.15 ( 16) SS BOND : angle 0.72646 / 0.57 ( 32) hydrogen bonds : bond 0.03789 / 2.51 ( 170) hydrogen bonds : angle 3.94107 / 2.56 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.9077 (ppp) cc_final: 0.7769 (ppp) REVERT: A 551 PHE cc_start: 0.9578 (t80) cc_final: 0.8777 (t80) REVERT: A 567 CYS cc_start: 0.7108 (OUTLIER) cc_final: 0.5975 (p) outliers start: 12 outliers final: 4 residues processed: 40 average time/residue: 0.0474 time to fit residues: 2.9371 Evaluate side-chains 38 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037914 restraints weight = 38320.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.039230 restraints weight = 27115.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.040182 restraints weight = 21065.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040923 restraints weight = 17415.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041485 restraints weight = 14997.561| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4823 Z= 0.091 Angle : 0.526 7.692 6501 Z= 0.252 Chirality : 0.037 0.179 705 Planarity : 0.003 0.029 842 Dihedral : 3.141 15.130 628 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.54 % Allowed : 14.01 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.36), residues: 580 helix: -0.36 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.030 0.001 TYR A 411 PHE 0.014 0.001 PHE A 395 TRP 0.006 0.001 TRP A 214 HIS 0.004 0.000 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 ( 4807) covalent geometry : angle 0.52549 / 0.25 ( 6469) SS BOND : bond 0.00149 / 0.12 ( 16) SS BOND : angle 0.57064 / 0.43 ( 32) hydrogen bonds : bond 0.03266 / 2.06 ( 170) hydrogen bonds : angle 3.75129 / 2.45 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.8778 (pt0) cc_final: 0.8551 (mt-10) REVERT: A 524 MET cc_start: 0.9083 (ppp) cc_final: 0.8672 (ppp) REVERT: A 528 PHE cc_start: 0.8541 (m-80) cc_final: 0.7936 (m-80) REVERT: A 567 CYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6198 (p) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.0489 time to fit residues: 2.7186 Evaluate side-chains 38 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.034988 restraints weight = 40624.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036205 restraints weight = 28301.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037132 restraints weight = 21871.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037819 restraints weight = 17982.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.038331 restraints weight = 15450.362| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4823 Z= 0.157 Angle : 0.567 8.944 6501 Z= 0.285 Chirality : 0.037 0.166 705 Planarity : 0.004 0.030 842 Dihedral : 3.367 21.740 628 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.30 % Allowed : 13.24 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.36), residues: 580 helix: -0.18 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 257 TYR 0.023 0.001 TYR A 411 PHE 0.011 0.001 PHE A 102 TRP 0.004 0.001 TRP A 214 HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 4807) covalent geometry : angle 0.56565 / 0.29 ( 6469) SS BOND : bond 0.00363 / 0.28 ( 16) SS BOND : angle 0.74279 / 0.54 ( 32) hydrogen bonds : bond 0.03094 / 2.05 ( 170) hydrogen bonds : angle 3.73670 / 2.48 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.9117 (ppp) cc_final: 0.8722 (ppp) REVERT: A 528 PHE cc_start: 0.8738 (m-80) cc_final: 0.8347 (m-80) REVERT: A 551 PHE cc_start: 0.9298 (t80) cc_final: 0.9024 (t80) REVERT: A 567 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.6736 (p) outliers start: 12 outliers final: 7 residues processed: 38 average time/residue: 0.0593 time to fit residues: 3.1055 Evaluate side-chains 37 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 17 optimal weight: 0.0060 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 12 optimal weight: 0.0570 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 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 = 0.3402 r_free = 0.3402 target = 0.049346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036313 restraints weight = 39679.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.037503 restraints weight = 28568.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038376 restraints weight = 22547.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039024 restraints weight = 18891.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039510 restraints weight = 16483.661| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4823 Z= 0.087 Angle : 0.539 8.975 6501 Z= 0.252 Chirality : 0.037 0.181 705 Planarity : 0.003 0.029 842 Dihedral : 3.167 15.758 628 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.15 % Allowed : 14.97 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.36), residues: 580 helix: 0.08 (0.31), residues: 312 sheet: None (None), residues: 0 loop : -0.90 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 257 TYR 0.026 0.001 TYR A 411 PHE 0.013 0.001 PHE A 488 TRP 0.006 0.001 TRP A 214 HIS 0.006 0.000 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 ( 4807) covalent geometry : angle 0.53935 / 0.25 ( 6469) SS BOND : bond 0.00177 / 0.14 ( 16) SS BOND : angle 0.55853 / 0.42 ( 32) hydrogen bonds : bond 0.02697 / 1.74 ( 170) hydrogen bonds : angle 3.52120 / 2.30 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.8952 (ppp) cc_final: 0.8387 (ppp) REVERT: A 528 PHE cc_start: 0.8734 (m-80) cc_final: 0.8191 (m-80) REVERT: A 548 MET cc_start: 0.9561 (pmm) cc_final: 0.9203 (pmm) REVERT: A 551 PHE cc_start: 0.9449 (t80) cc_final: 0.9114 (t80) REVERT: A 567 CYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6064 (p) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.0609 time to fit residues: 3.1296 Evaluate side-chains 36 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 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 = 0.3360 r_free = 0.3360 target = 0.047897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.035312 restraints weight = 40073.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.036457 restraints weight = 28996.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037287 restraints weight = 22963.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.037935 restraints weight = 19291.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038416 restraints weight = 16806.956| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4823 Z= 0.118 Angle : 0.561 10.181 6501 Z= 0.272 Chirality : 0.037 0.173 705 Planarity : 0.003 0.030 842 Dihedral : 3.245 16.890 628 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.34 % Allowed : 15.55 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.37), residues: 580 helix: 0.21 (0.31), residues: 327 sheet: None (None), residues: 0 loop : -0.82 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.023 0.001 TYR A 411 PHE 0.007 0.001 PHE A 27 TRP 0.004 0.001 TRP A 214 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 4807) covalent geometry : angle 0.56052 / 0.27 ( 6469) SS BOND : bond 0.00258 / 0.20 ( 16) SS BOND : angle 0.69083 / 0.52 ( 32) hydrogen bonds : bond 0.02712 / 1.74 ( 170) hydrogen bonds : angle 3.55746 / 2.33 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.9036 (ppp) cc_final: 0.8423 (ppp) REVERT: A 528 PHE cc_start: 0.8764 (m-80) cc_final: 0.8294 (m-80) REVERT: A 551 PHE cc_start: 0.9284 (t80) cc_final: 0.9052 (t80) REVERT: A 567 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6108 (p) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.0594 time to fit residues: 2.9092 Evaluate side-chains 34 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 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 = 0.3365 r_free = 0.3365 target = 0.048021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.035342 restraints weight = 40375.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.036506 restraints weight = 28981.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037379 restraints weight = 22872.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.038039 restraints weight = 19134.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038533 restraints weight = 16653.438| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4823 Z= 0.092 Angle : 0.563 10.307 6501 Z= 0.266 Chirality : 0.037 0.182 705 Planarity : 0.003 0.029 842 Dihedral : 3.172 15.805 628 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.54 % Allowed : 15.36 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.37), residues: 580 helix: 0.34 (0.31), residues: 326 sheet: None (None), residues: 0 loop : -0.76 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.022 0.001 TYR A 411 PHE 0.014 0.001 PHE A 488 TRP 0.005 0.001 TRP A 214 HIS 0.001 0.000 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 4807) covalent geometry : angle 0.56256 / 0.27 ( 6469) SS BOND : bond 0.00192 / 0.15 ( 16) SS BOND : angle 0.58521 / 0.44 ( 32) hydrogen bonds : bond 0.02497 / 1.62 ( 170) hydrogen bonds : angle 3.47283 / 2.27 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9323 (tp40) cc_final: 0.9089 (tp40) REVERT: A 448 CYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8298 (m) REVERT: A 524 MET cc_start: 0.9036 (ppp) cc_final: 0.8398 (ppp) REVERT: A 528 PHE cc_start: 0.8824 (m-80) cc_final: 0.8263 (m-80) REVERT: A 551 PHE cc_start: 0.9367 (t80) cc_final: 0.9076 (t80) REVERT: A 567 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6590 (p) outliers start: 8 outliers final: 6 residues processed: 36 average time/residue: 0.0549 time to fit residues: 2.9306 Evaluate side-chains 38 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 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 = 0.3362 r_free = 0.3362 target = 0.047679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.035051 restraints weight = 39767.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036237 restraints weight = 28353.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036980 restraints weight = 22275.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.037692 restraints weight = 18948.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038221 restraints weight = 16396.843| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4823 Z= 0.095 Angle : 0.569 10.801 6501 Z= 0.268 Chirality : 0.037 0.180 705 Planarity : 0.003 0.030 842 Dihedral : 3.171 15.131 628 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.92 % Allowed : 15.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.38), residues: 580 helix: 0.45 (0.31), residues: 333 sheet: None (None), residues: 0 loop : -0.72 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.021 0.001 TYR A 411 PHE 0.007 0.001 PHE A 395 TRP 0.005 0.001 TRP A 214 HIS 0.001 0.000 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 ( 4807) covalent geometry : angle 0.56862 / 0.27 ( 6469) SS BOND : bond 0.00200 / 0.15 ( 16) SS BOND : angle 0.59537 / 0.44 ( 32) hydrogen bonds : bond 0.02411 / 1.56 ( 170) hydrogen bonds : angle 3.43537 / 2.24 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9316 (tp40) cc_final: 0.9080 (tp40) REVERT: A 448 CYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8410 (m) REVERT: A 524 MET cc_start: 0.9046 (ppp) cc_final: 0.8682 (ptt) REVERT: A 528 PHE cc_start: 0.8972 (m-80) cc_final: 0.8597 (m-80) REVERT: A 544 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9275 (pt) REVERT: A 551 PHE cc_start: 0.9519 (t80) cc_final: 0.9299 (t80) REVERT: A 567 CYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6657 (p) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.0601 time to fit residues: 3.2457 Evaluate side-chains 38 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.0010 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.0470 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 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 = 0.3364 r_free = 0.3364 target = 0.047717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.035112 restraints weight = 39488.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036301 restraints weight = 28221.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037054 restraints weight = 22168.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.037717 restraints weight = 18867.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038280 restraints weight = 16452.217| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4823 Z= 0.091 Angle : 0.575 12.439 6501 Z= 0.266 Chirality : 0.038 0.184 705 Planarity : 0.003 0.029 842 Dihedral : 3.124 14.693 628 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.73 % Allowed : 15.36 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.38), residues: 580 helix: 0.53 (0.31), residues: 336 sheet: None (None), residues: 0 loop : -0.55 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.021 0.001 TYR A 411 PHE 0.007 0.001 PHE A 395 TRP 0.005 0.001 TRP A 214 HIS 0.001 0.000 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 4807) covalent geometry : angle 0.57538 / 0.27 ( 6469) SS BOND : bond 0.00177 / 0.14 ( 16) SS BOND : angle 0.53438 / 0.41 ( 32) hydrogen bonds : bond 0.02286 / 1.47 ( 170) hydrogen bonds : angle 3.36454 / 2.18 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7848 (mmm) cc_final: 0.7028 (mmm) REVERT: A 411 TYR cc_start: 0.9577 (m-80) cc_final: 0.9218 (m-80) REVERT: A 415 MET cc_start: 0.9358 (tmm) cc_final: 0.9100 (tmm) REVERT: A 448 CYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 524 MET cc_start: 0.9043 (ppp) cc_final: 0.8372 (ppp) REVERT: A 528 PHE cc_start: 0.8983 (m-80) cc_final: 0.8539 (m-80) REVERT: A 544 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9281 (pt) REVERT: A 551 PHE cc_start: 0.9509 (t80) cc_final: 0.9158 (t80) REVERT: A 567 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6692 (p) outliers start: 9 outliers final: 5 residues processed: 35 average time/residue: 0.0592 time to fit residues: 3.0988 Evaluate side-chains 36 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 31 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 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 = 0.3375 r_free = 0.3375 target = 0.047937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.035395 restraints weight = 40187.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.036561 restraints weight = 28761.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037471 restraints weight = 22610.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.038123 restraints weight = 18820.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038643 restraints weight = 16337.306| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4823 Z= 0.098 Angle : 0.595 11.899 6501 Z= 0.280 Chirality : 0.038 0.185 705 Planarity : 0.003 0.029 842 Dihedral : 3.274 22.916 628 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.34 % Allowed : 15.74 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.38), residues: 580 helix: 0.47 (0.31), residues: 342 sheet: None (None), residues: 0 loop : -0.66 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.020 0.001 TYR A 411 PHE 0.008 0.001 PHE A 395 TRP 0.005 0.001 TRP A 214 HIS 0.001 0.000 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 4807) covalent geometry : angle 0.59477 / 0.28 ( 6469) SS BOND : bond 0.00168 / 0.13 ( 16) SS BOND : angle 0.56731 / 0.44 ( 32) hydrogen bonds : bond 0.02302 / 1.50 ( 170) hydrogen bonds : angle 3.31371 / 2.13 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.06 seconds wall clock time: 17 minutes 42.96 seconds (1062.96 seconds total)