Starting phenix.real_space_refine on Fri Sep 11 11:24:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j5u_0681/09_2026/6j5u_0681.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j5u_0681/09_2026/6j5u_0681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j5u_0681/09_2026/6j5u_0681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j5u_0681/09_2026/6j5u_0681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j5u_0681/09_2026/6j5u_0681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j5u_0681/09_2026/6j5u_0681.map" } resolution = 3.9 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 59 5.16 5 C 5895 2.51 5 N 1585 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9288 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5266 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 26, 'TRANS': 636} Chain breaks: 2 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1340 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 4 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BQL C 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL C 501 " occ=0.00 Time building chain proxies: 2.08, per 1000 atoms: 0.22 Number of scatterers: 9288 At special positions: 0 Unit cell: (88.371, 92.735, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 2 15.00 O 1747 8.00 N 1585 7.00 C 5895 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 additional links: simple=2, symmetry=0 Simple link: pdb=" C VAL C 252 " - pdb=" N BQL C 501 " Simple link: pdb=" N LYS C 255 " - pdb=" C BQO C 502 " Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 353.2 milliseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 41.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.659A pdb=" N VAL A 6 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 31 through 42 removed outlier: 5.364A pdb=" N GLU A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.617A pdb=" N ARG A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 81 removed outlier: 3.531A pdb=" N TYR A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.525A pdb=" N SER A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.713A pdb=" N TRP A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.559A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 removed outlier: 4.087A pdb=" N TRP A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.858A pdb=" N CYS A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.749A pdb=" N LEU A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 425' Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.936A pdb=" N HIS A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 removed outlier: 4.061A pdb=" N ASP A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.042A pdb=" N LEU A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 removed outlier: 4.082A pdb=" N ALA A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.675A pdb=" N ILE A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 631 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 removed outlier: 3.527A pdb=" N LEU A 657 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.562A pdb=" N VAL A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 4.148A pdb=" N ASP A 705 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.889A pdb=" N LYS A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.914A pdb=" N PHE C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 292 removed outlier: 3.928A pdb=" N ASP C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.716A pdb=" N THR C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.080A pdb=" N GLN C 335 " --> pdb=" O GLN C 332 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 336 " --> pdb=" O TYR C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 332 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 361 through 367 removed outlier: 4.108A pdb=" N THR C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.591A pdb=" N SER B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 4.011A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 97 through 115 removed outlier: 3.855A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 182 removed outlier: 3.615A pdb=" N ARG B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.955A pdb=" N TYR B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.856A pdb=" N ARG B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 308 through 322 removed outlier: 3.577A pdb=" N VAL B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 344 through 347 Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA2, first strand: chain 'A' and resid 515 through 518 removed outlier: 6.726A pdb=" N LEU A 515 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR A 538 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 517 " --> pdb=" O THR A 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.952A pdb=" N ASN A 545 " --> pdb=" O ILE A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.567A pdb=" N LEU A 591 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 640 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 663 " --> pdb=" O GLY A 690 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 689 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 716 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 796 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.591A pdb=" N TRP B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY B 125 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 189 removed outlier: 3.618A pdb=" N ILE B 186 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 223 281 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1562 1.31 - 1.44: 2405 1.44 - 1.57: 5410 1.57 - 1.69: 6 1.69 - 1.82: 86 Bond restraints: 9469 Sorted by residual: bond pdb=" OP3 BQO C 502 " pdb=" P BQO C 502 " ideal model delta sigma weight residual 1.494 1.646 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C1' BQO C 502 " pdb=" O4' BQO C 502 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C4 BQO C 502 " pdb=" C5 BQO C 502 " ideal model delta sigma weight residual 1.439 1.354 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N VAL A 400 " pdb=" CA VAL A 400 " ideal model delta sigma weight residual 1.459 1.493 -0.034 9.10e-03 1.21e+04 1.42e+01 bond pdb=" C4 BQO C 502 " pdb=" N3 BQO C 502 " ideal model delta sigma weight residual 1.389 1.323 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 9464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 12147 2.77 - 5.53: 526 5.53 - 8.30: 88 8.30 - 11.06: 26 11.06 - 13.83: 14 Bond angle restraints: 12801 Sorted by residual: angle pdb=" C ALA B 182 " pdb=" N PHE B 183 " pdb=" CA PHE B 183 " ideal model delta sigma weight residual 123.96 116.27 7.69 1.44e+00 4.82e-01 2.85e+01 angle pdb=" N VAL A 631 " pdb=" CA VAL A 631 " pdb=" C VAL A 631 " ideal model delta sigma weight residual 112.29 107.40 4.89 9.40e-01 1.13e+00 2.71e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 113.47 108.69 4.78 1.01e+00 9.80e-01 2.24e+01 angle pdb=" CA THR A 541 " pdb=" CB THR A 541 " pdb=" CG2 THR A 541 " ideal model delta sigma weight residual 110.50 118.53 -8.03 1.70e+00 3.46e-01 2.23e+01 angle pdb=" C GLY B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 12796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.44: 4998 15.44 - 30.88: 603 30.88 - 46.33: 169 46.33 - 61.77: 16 61.77 - 77.21: 10 Dihedral angle restraints: 5796 sinusoidal: 2414 harmonic: 3382 Sorted by residual: dihedral pdb=" CA LYS A 531 " pdb=" C LYS A 531 " pdb=" N LEU A 532 " pdb=" CA LEU A 532 " ideal model delta harmonic sigma weight residual 180.00 141.69 38.31 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA CYS A 649 " pdb=" C CYS A 649 " pdb=" N PHE A 650 " pdb=" CA PHE A 650 " ideal model delta harmonic sigma weight residual 180.00 143.18 36.82 0 5.00e+00 4.00e-02 5.42e+01 dihedral pdb=" CA GLU C 266 " pdb=" C GLU C 266 " pdb=" N TYR C 267 " pdb=" CA TYR C 267 " ideal model delta harmonic sigma weight residual 180.00 145.84 34.16 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 5793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1060 0.073 - 0.147: 316 0.147 - 0.220: 60 0.220 - 0.294: 11 0.294 - 0.367: 2 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CB THR C 190 " pdb=" CA THR C 190 " pdb=" OG1 THR C 190 " pdb=" CG2 THR C 190 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE A 614 " pdb=" CA ILE A 614 " pdb=" CG1 ILE A 614 " pdb=" CG2 ILE A 614 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' BQO C 502 " pdb=" C1' BQO C 502 " pdb=" C3' BQO C 502 " pdb=" O1 BQO C 502 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1446 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 44 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 525 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLN A 525 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN A 525 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 526 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO A 102 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.041 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 71 2.45 - 3.07: 5882 3.07 - 3.68: 15758 3.68 - 4.29: 21360 4.29 - 4.90: 33435 Nonbonded interactions: 76506 Sorted by model distance: nonbonded pdb=" O GLU A 396 " pdb=" ND2 ASN A 399 " model vdw 1.843 2.496 nonbonded pdb=" O PHE C 182 " pdb=" N ARG C 184 " model vdw 1.936 3.120 nonbonded pdb=" O SER A 395 " pdb=" CG ASN A 399 " model vdw 1.946 3.270 nonbonded pdb=" O SER A 395 " pdb=" OD1 ASN A 399 " model vdw 2.001 3.040 nonbonded pdb=" C SER A 395 " pdb=" OD1 ASN A 399 " model vdw 2.013 3.270 ... (remaining 76501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 0.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.009 0.169 9472 Z= 0.429 Angle : 1.397 13.827 12807 Z= 0.706 Chirality : 0.073 0.367 1449 Planarity : 0.008 0.089 1621 Dihedral : 14.539 77.207 3596 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.36 % Favored : 85.29 % Rotamer: Outliers : 2.32 % Allowed : 12.17 % Favored : 85.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.13 (0.20), residues: 1142 helix: -3.59 (0.16), residues: 414 sheet: -3.38 (0.51), residues: 88 loop : -3.37 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG A 695 TYR 0.047 0.003 TYR A 560 PHE 0.031 0.004 PHE B 232 TRP 0.025 0.004 TRP B 162 HIS 0.012 0.003 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.39 ( 9469) covalent geometry : angle 1.39735 / 0.71 (12801) hydrogen bonds : bond 0.18539 / 11.08 ( 281) hydrogen bonds : angle 8.93007 / 6.34 ( 774) Misc. bond : bond 0.16911 / 8.90 ( 1) link_TRANS : bond 0.00234 / 0.12 ( 2) link_TRANS : angle 1.14348 / 0.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 323 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7644 (p90) cc_final: 0.6901 (p90) REVERT: A 351 ILE cc_start: 0.9141 (mp) cc_final: 0.8689 (mm) REVERT: A 359 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.7782 (Cg_endo) REVERT: A 381 ARG cc_start: 0.8873 (tmt90) cc_final: 0.8608 (ttp-110) REVERT: A 425 TYR cc_start: 0.7944 (m-80) cc_final: 0.7655 (m-10) REVERT: A 435 GLN cc_start: 0.8037 (mt0) cc_final: 0.7639 (tp-100) REVERT: A 513 ARG cc_start: 0.6683 (tpm170) cc_final: 0.6410 (tpp-160) REVERT: A 614 ILE cc_start: 0.8837 (pp) cc_final: 0.8576 (pt) REVERT: A 746 LEU cc_start: 0.8534 (pt) cc_final: 0.8289 (pt) REVERT: C 184 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7149 (tpt-90) REVERT: C 196 LYS cc_start: 0.7193 (mttt) cc_final: 0.6724 (mmtm) REVERT: C 267 TYR cc_start: 0.8045 (t80) cc_final: 0.7705 (t80) REVERT: B 114 MET cc_start: 0.7710 (tpp) cc_final: 0.6822 (tpp) REVERT: B 164 VAL cc_start: 0.9130 (m) cc_final: 0.8642 (t) REVERT: B 168 ILE cc_start: 0.9523 (pt) cc_final: 0.8937 (mt) REVERT: B 171 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 190 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6976 (ptt90) REVERT: B 192 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8590 (m) REVERT: B 201 LYS cc_start: 0.8682 (pptt) cc_final: 0.7959 (tttp) REVERT: B 202 ASN cc_start: 0.8634 (t0) cc_final: 0.8420 (t0) REVERT: B 342 GLN cc_start: 0.7931 (pp30) cc_final: 0.7718 (pp30) outliers start: 24 outliers final: 10 residues processed: 337 average time/residue: 0.0988 time to fit residues: 45.2667 Evaluate side-chains 227 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 35 GLN A 329 ASN A 377 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 488 HIS A 525 GLN A 627 GLN A 643 ASN A 673 ASN C 343 ASN C 350 ASN B 39 ASN B 52 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.143056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113470 restraints weight = 19324.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116785 restraints weight = 11437.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.118996 restraints weight = 7987.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.120494 restraints weight = 6265.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121413 restraints weight = 5319.259| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9472 Z= 0.153 Angle : 0.875 13.610 12807 Z= 0.434 Chirality : 0.050 0.290 1449 Planarity : 0.006 0.081 1621 Dihedral : 11.098 83.464 1346 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 5.70 % Allowed : 17.39 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.18 % 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: -4.33 (0.21), residues: 1142 helix: -2.46 (0.21), residues: 436 sheet: -3.09 (0.55), residues: 76 loop : -3.26 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 695 TYR 0.028 0.002 TYR B 105 PHE 0.022 0.002 PHE A 633 TRP 0.024 0.002 TRP B 227 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9469) covalent geometry : angle 0.87493 / 0.43 (12801) hydrogen bonds : bond 0.04321 / 2.74 ( 281) hydrogen bonds : angle 6.58797 / 4.70 ( 774) Misc. bond : bond 0.00167 / 0.09 ( 1) link_TRANS : bond 0.00178 / 0.08 ( 2) link_TRANS : angle 0.61410 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8269 (tppp) cc_final: 0.8033 (tttm) REVERT: A 77 VAL cc_start: 0.8234 (t) cc_final: 0.7946 (t) REVERT: A 149 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8429 (mtm110) REVERT: A 344 LEU cc_start: 0.7851 (mt) cc_final: 0.7585 (pp) REVERT: A 351 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 359 PRO cc_start: 0.8913 (Cg_exo) cc_final: 0.8137 (Cg_endo) REVERT: A 363 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8523 (mmtt) REVERT: A 381 ARG cc_start: 0.8917 (tmt90) cc_final: 0.8607 (tmm-80) REVERT: A 401 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8459 (tpt) REVERT: A 417 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8758 (t) REVERT: A 443 GLU cc_start: 0.6140 (pp20) cc_final: 0.5907 (pp20) REVERT: A 459 GLU cc_start: 0.8385 (pp20) cc_final: 0.8125 (tp30) REVERT: A 546 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7548 (mmtp) REVERT: A 688 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8412 (mtpp) REVERT: A 721 TYR cc_start: 0.5933 (t80) cc_final: 0.4401 (t80) REVERT: A 724 TYR cc_start: 0.6801 (m-10) cc_final: 0.6015 (m-10) REVERT: A 730 THR cc_start: 0.8203 (m) cc_final: 0.7936 (m) REVERT: A 763 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8549 (mt) REVERT: C 176 SER cc_start: 0.8545 (p) cc_final: 0.8296 (p) REVERT: C 196 LYS cc_start: 0.7038 (mttt) cc_final: 0.6732 (mmtm) REVERT: C 359 MET cc_start: 0.7245 (tpp) cc_final: 0.6278 (pmm) REVERT: B 114 MET cc_start: 0.7876 (tpp) cc_final: 0.7089 (mpp) REVERT: B 160 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8067 (pp) REVERT: B 164 VAL cc_start: 0.8961 (m) cc_final: 0.8589 (t) REVERT: B 168 ILE cc_start: 0.9458 (pt) cc_final: 0.8786 (mt) REVERT: B 170 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8500 (pmtt) REVERT: B 342 GLN cc_start: 0.7816 (pp30) cc_final: 0.7518 (pp30) outliers start: 59 outliers final: 24 residues processed: 292 average time/residue: 0.0943 time to fit residues: 38.0738 Evaluate side-chains 232 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS A 786 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113129 restraints weight = 19245.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116467 restraints weight = 11266.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.118712 restraints weight = 7817.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.120235 restraints weight = 6119.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.121135 restraints weight = 5174.382| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9472 Z= 0.142 Angle : 0.831 13.615 12807 Z= 0.407 Chirality : 0.049 0.239 1449 Planarity : 0.005 0.075 1621 Dihedral : 9.839 85.597 1334 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 6.38 % Allowed : 18.74 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.79 (0.22), residues: 1142 helix: -1.97 (0.22), residues: 434 sheet: -2.96 (0.58), residues: 71 loop : -2.95 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 104 TYR 0.032 0.002 TYR B 105 PHE 0.015 0.002 PHE A 633 TRP 0.020 0.002 TRP B 227 HIS 0.011 0.002 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9469) covalent geometry : angle 0.83077 / 0.41 (12801) hydrogen bonds : bond 0.04035 / 2.61 ( 281) hydrogen bonds : angle 6.05861 / 4.30 ( 774) Misc. bond : bond 0.00130 / 0.07 ( 1) link_TRANS : bond 0.00103 / 0.05 ( 2) link_TRANS : angle 0.45408 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7504 (p90) cc_final: 0.6747 (p90) REVERT: A 149 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8162 (mtm110) REVERT: A 359 PRO cc_start: 0.8827 (Cg_exo) cc_final: 0.7986 (Cg_endo) REVERT: A 435 GLN cc_start: 0.8257 (mt0) cc_final: 0.7905 (tt0) REVERT: A 688 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8390 (mtpp) REVERT: A 689 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7838 (tt) REVERT: A 730 THR cc_start: 0.8224 (m) cc_final: 0.7982 (m) REVERT: A 790 HIS cc_start: 0.7089 (m90) cc_final: 0.6804 (m90) REVERT: A 804 LEU cc_start: 0.8468 (mm) cc_final: 0.8003 (mp) REVERT: A 829 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7622 (tm) REVERT: C 178 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: C 196 LYS cc_start: 0.7093 (mttt) cc_final: 0.6741 (mmtm) REVERT: C 293 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7733 (mtm180) REVERT: C 355 LEU cc_start: 0.7368 (pp) cc_final: 0.6261 (tt) REVERT: C 361 GLU cc_start: 0.8490 (tt0) cc_final: 0.7657 (tm-30) REVERT: B 122 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 123 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8501 (tt) REVERT: B 164 VAL cc_start: 0.8941 (m) cc_final: 0.8620 (t) REVERT: B 168 ILE cc_start: 0.9405 (pt) cc_final: 0.8696 (mt) REVERT: B 170 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8503 (pmtt) REVERT: B 333 MET cc_start: 0.7451 (mmm) cc_final: 0.7052 (mmm) REVERT: B 342 GLN cc_start: 0.7847 (pp30) cc_final: 0.7536 (pp30) outliers start: 66 outliers final: 34 residues processed: 275 average time/residue: 0.0977 time to fit residues: 37.6554 Evaluate side-chains 237 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 96 optimal weight: 0.0170 chunk 112 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS A 622 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.109133 restraints weight = 19617.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.112302 restraints weight = 11692.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114396 restraints weight = 8234.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115870 restraints weight = 6496.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116811 restraints weight = 5518.192| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9472 Z= 0.171 Angle : 0.835 14.861 12807 Z= 0.409 Chirality : 0.050 0.233 1449 Planarity : 0.005 0.077 1621 Dihedral : 9.586 89.690 1334 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 6.28 % Allowed : 22.22 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.57 (0.23), residues: 1142 helix: -1.71 (0.22), residues: 443 sheet: -3.21 (0.54), residues: 71 loop : -2.84 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 695 TYR 0.025 0.002 TYR B 105 PHE 0.028 0.002 PHE B 244 TRP 0.023 0.002 TRP B 227 HIS 0.009 0.002 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9469) covalent geometry : angle 0.83513 / 0.41 (12801) hydrogen bonds : bond 0.03938 / 2.54 ( 281) hydrogen bonds : angle 6.00118 / 4.27 ( 774) Misc. bond : bond 0.00087 / 0.05 ( 1) link_TRANS : bond 0.00249 / 0.12 ( 2) link_TRANS : angle 0.54319 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 214 time to evaluate : 0.411 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 67 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8277 (mm-30) REVERT: A 149 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.7809 (ttp-110) REVERT: A 435 GLN cc_start: 0.8370 (mt0) cc_final: 0.8032 (tt0) REVERT: A 632 LEU cc_start: 0.7988 (mm) cc_final: 0.7774 (mm) REVERT: A 688 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8435 (mtpp) REVERT: A 832 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: C 196 LYS cc_start: 0.7430 (mttt) cc_final: 0.7090 (mmtm) REVERT: C 293 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7500 (mtm180) REVERT: C 355 LEU cc_start: 0.7455 (pp) cc_final: 0.6195 (tt) REVERT: C 361 GLU cc_start: 0.8428 (tt0) cc_final: 0.7747 (tm-30) REVERT: B 22 TRP cc_start: 0.8030 (m-10) cc_final: 0.7792 (m-10) REVERT: B 114 MET cc_start: 0.7934 (tpp) cc_final: 0.7041 (mpp) REVERT: B 164 VAL cc_start: 0.9004 (m) cc_final: 0.8642 (t) REVERT: B 166 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8610 (tm) REVERT: B 168 ILE cc_start: 0.9435 (pt) cc_final: 0.8771 (mt) REVERT: B 170 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8544 (pmtt) REVERT: B 201 LYS cc_start: 0.8398 (pptt) cc_final: 0.8028 (mttt) REVERT: B 342 GLN cc_start: 0.8000 (pp30) cc_final: 0.7676 (pp30) outliers start: 65 outliers final: 39 residues processed: 262 average time/residue: 0.0869 time to fit residues: 32.0904 Evaluate side-chains 233 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112847 restraints weight = 19586.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115974 restraints weight = 11901.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118106 restraints weight = 8434.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119583 restraints weight = 6651.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.120479 restraints weight = 5656.579| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9472 Z= 0.141 Angle : 0.826 14.276 12807 Z= 0.399 Chirality : 0.049 0.222 1449 Planarity : 0.005 0.075 1621 Dihedral : 9.243 83.796 1334 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 5.60 % Allowed : 24.06 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.24), residues: 1142 helix: -1.42 (0.24), residues: 434 sheet: -3.33 (0.51), residues: 71 loop : -2.63 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 695 TYR 0.019 0.002 TYR B 239 PHE 0.028 0.002 PHE A 445 TRP 0.021 0.002 TRP A 150 HIS 0.009 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9469) covalent geometry : angle 0.82613 / 0.40 (12801) hydrogen bonds : bond 0.03870 / 2.50 ( 281) hydrogen bonds : angle 5.81391 / 4.18 ( 774) Misc. bond : bond 0.00095 / 0.05 ( 1) link_TRANS : bond 0.00114 / 0.06 ( 2) link_TRANS : angle 0.45375 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7892 (mmtt) REVERT: A 376 TYR cc_start: 0.8167 (t80) cc_final: 0.7558 (t80) REVERT: A 435 GLN cc_start: 0.8382 (mt0) cc_final: 0.8060 (tt0) REVERT: A 763 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 786 ASN cc_start: 0.5807 (m110) cc_final: 0.5539 (m-40) REVERT: A 815 MET cc_start: 0.8280 (mtm) cc_final: 0.8078 (mtm) REVERT: A 832 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: C 178 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: C 196 LYS cc_start: 0.7360 (mttt) cc_final: 0.7074 (mmtm) REVERT: C 293 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7566 (mtm180) REVERT: C 361 GLU cc_start: 0.8391 (tt0) cc_final: 0.7777 (tm-30) REVERT: B 114 MET cc_start: 0.7857 (tpp) cc_final: 0.7135 (mpp) REVERT: B 164 VAL cc_start: 0.8971 (m) cc_final: 0.8624 (t) REVERT: B 166 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8675 (tm) REVERT: B 168 ILE cc_start: 0.9379 (pt) cc_final: 0.8686 (mt) REVERT: B 170 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (pmtt) REVERT: B 201 LYS cc_start: 0.8332 (pptt) cc_final: 0.7948 (mttt) REVERT: B 282 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 342 GLN cc_start: 0.7962 (pp30) cc_final: 0.7639 (pp30) outliers start: 58 outliers final: 36 residues processed: 250 average time/residue: 0.0905 time to fit residues: 31.7424 Evaluate side-chains 225 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111602 restraints weight = 19637.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114784 restraints weight = 11637.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117003 restraints weight = 8182.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.118505 restraints weight = 6411.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.119419 restraints weight = 5429.855| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9472 Z= 0.147 Angle : 0.833 13.901 12807 Z= 0.404 Chirality : 0.049 0.228 1449 Planarity : 0.005 0.067 1621 Dihedral : 9.202 84.375 1334 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 5.22 % Allowed : 24.64 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.13 (0.24), residues: 1142 helix: -1.36 (0.24), residues: 442 sheet: -3.35 (0.52), residues: 71 loop : -2.52 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 695 TYR 0.017 0.001 TYR B 105 PHE 0.020 0.002 PHE A 521 TRP 0.032 0.002 TRP A 379 HIS 0.009 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 9469) covalent geometry : angle 0.83315 / 0.40 (12801) hydrogen bonds : bond 0.03779 / 2.43 ( 281) hydrogen bonds : angle 5.70118 / 4.09 ( 774) Misc. bond : bond 0.00035 / 0.02 ( 1) link_TRANS : bond 0.00124 / 0.06 ( 2) link_TRANS : angle 0.57236 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8489 (mm-30) REVERT: A 356 LYS cc_start: 0.8650 (mmpt) cc_final: 0.8444 (mmpt) REVERT: A 376 TYR cc_start: 0.8063 (t80) cc_final: 0.7695 (t80) REVERT: A 401 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8095 (tpp) REVERT: A 435 GLN cc_start: 0.8359 (mt0) cc_final: 0.8008 (tt0) REVERT: A 763 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 815 MET cc_start: 0.8290 (mtm) cc_final: 0.8066 (mtm) REVERT: A 832 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: C 196 LYS cc_start: 0.7368 (mttt) cc_final: 0.7087 (mmtm) REVERT: C 293 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7577 (mtm180) REVERT: C 323 ARG cc_start: 0.7619 (tpt90) cc_final: 0.7342 (mmt180) REVERT: C 325 MET cc_start: 0.6990 (pp-130) cc_final: 0.6722 (pp-130) REVERT: C 361 GLU cc_start: 0.8368 (tt0) cc_final: 0.7802 (tm-30) REVERT: B 114 MET cc_start: 0.7888 (tpp) cc_final: 0.7121 (mpp) REVERT: B 164 VAL cc_start: 0.8990 (m) cc_final: 0.8658 (t) REVERT: B 166 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8718 (tm) REVERT: B 168 ILE cc_start: 0.9366 (pt) cc_final: 0.8732 (mt) REVERT: B 170 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (pmtt) REVERT: B 201 LYS cc_start: 0.8408 (pptt) cc_final: 0.8093 (mttp) REVERT: B 342 GLN cc_start: 0.7997 (pp30) cc_final: 0.7653 (pp30) outliers start: 54 outliers final: 38 residues processed: 241 average time/residue: 0.0833 time to fit residues: 28.7021 Evaluate side-chains 231 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105129 restraints weight = 19684.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108151 restraints weight = 11856.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110194 restraints weight = 8385.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111524 restraints weight = 6659.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112212 restraints weight = 5712.638| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9472 Z= 0.233 Angle : 0.886 15.992 12807 Z= 0.439 Chirality : 0.052 0.207 1449 Planarity : 0.005 0.069 1621 Dihedral : 9.141 81.594 1334 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 5.60 % Allowed : 25.31 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.33 (0.23), residues: 1142 helix: -1.43 (0.23), residues: 442 sheet: -3.16 (0.54), residues: 73 loop : -2.75 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 695 TYR 0.022 0.002 TYR C 267 PHE 0.022 0.002 PHE B 130 TRP 0.027 0.003 TRP A 379 HIS 0.012 0.002 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 ( 9469) covalent geometry : angle 0.88600 / 0.44 (12801) hydrogen bonds : bond 0.04108 / 2.65 ( 281) hydrogen bonds : angle 5.88702 / 4.21 ( 774) Misc. bond : bond 0.00017 / 0.01 ( 1) link_TRANS : bond 0.00241 / 0.12 ( 2) link_TRANS : angle 0.40823 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8506 (mm-30) REVERT: A 376 TYR cc_start: 0.8192 (t80) cc_final: 0.7804 (t80) REVERT: A 417 SER cc_start: 0.8998 (t) cc_final: 0.8698 (t) REVERT: A 435 GLN cc_start: 0.8475 (mt0) cc_final: 0.8126 (tt0) REVERT: A 714 MET cc_start: 0.6456 (tpp) cc_final: 0.6140 (mmm) REVERT: A 763 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8764 (mt) REVERT: A 815 MET cc_start: 0.8250 (mtm) cc_final: 0.8017 (mtp) REVERT: A 832 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: C 196 LYS cc_start: 0.7450 (mttt) cc_final: 0.7114 (mmtm) REVERT: C 293 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7223 (mtm180) REVERT: C 361 GLU cc_start: 0.8413 (tt0) cc_final: 0.7855 (tm-30) REVERT: B 114 MET cc_start: 0.7994 (tpp) cc_final: 0.7223 (mpp) REVERT: B 164 VAL cc_start: 0.9057 (m) cc_final: 0.8718 (t) REVERT: B 166 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8745 (tm) REVERT: B 168 ILE cc_start: 0.9500 (pt) cc_final: 0.8958 (mt) REVERT: B 170 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8565 (pmtt) REVERT: B 342 GLN cc_start: 0.8074 (pp30) cc_final: 0.7782 (pp30) outliers start: 58 outliers final: 38 residues processed: 232 average time/residue: 0.0845 time to fit residues: 27.9821 Evaluate side-chains 219 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111993 restraints weight = 19491.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115164 restraints weight = 11592.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117410 restraints weight = 8173.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118796 restraints weight = 6411.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.119918 restraints weight = 5465.730| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9472 Z= 0.142 Angle : 0.848 14.247 12807 Z= 0.411 Chirality : 0.051 0.254 1449 Planarity : 0.005 0.066 1621 Dihedral : 8.467 81.395 1330 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 4.64 % Allowed : 26.67 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.95 (0.24), residues: 1142 helix: -1.13 (0.25), residues: 432 sheet: -2.61 (0.60), residues: 61 loop : -2.58 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 695 TYR 0.018 0.001 TYR B 239 PHE 0.023 0.002 PHE B 130 TRP 0.019 0.001 TRP A 379 HIS 0.009 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9469) covalent geometry : angle 0.84831 / 0.41 (12801) hydrogen bonds : bond 0.03720 / 2.39 ( 281) hydrogen bonds : angle 5.64977 / 4.07 ( 774) Misc. bond : bond 0.00032 / 0.02 ( 1) link_TRANS : bond 0.00164 / 0.08 ( 2) link_TRANS : angle 0.36137 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8121 (t80) cc_final: 0.7779 (t80) REVERT: A 401 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8263 (tpt) REVERT: A 417 SER cc_start: 0.8955 (t) cc_final: 0.8630 (t) REVERT: A 701 GLU cc_start: 0.8105 (mp0) cc_final: 0.7444 (pp20) REVERT: A 815 MET cc_start: 0.8086 (mtm) cc_final: 0.7854 (mtm) REVERT: A 832 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: C 196 LYS cc_start: 0.7371 (mttt) cc_final: 0.7096 (mmtm) REVERT: C 267 TYR cc_start: 0.8037 (t80) cc_final: 0.7657 (t80) REVERT: C 272 ARG cc_start: 0.7535 (ptm160) cc_final: 0.6980 (ptp-170) REVERT: C 361 GLU cc_start: 0.8360 (tt0) cc_final: 0.7866 (tm-30) REVERT: B 63 SER cc_start: 0.8041 (m) cc_final: 0.7758 (p) REVERT: B 114 MET cc_start: 0.7779 (tpp) cc_final: 0.7122 (mpp) REVERT: B 164 VAL cc_start: 0.8963 (m) cc_final: 0.8580 (t) REVERT: B 166 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8690 (tm) REVERT: B 168 ILE cc_start: 0.9421 (pt) cc_final: 0.8727 (mt) REVERT: B 177 THR cc_start: 0.8927 (m) cc_final: 0.8714 (t) REVERT: B 201 LYS cc_start: 0.8240 (mttt) cc_final: 0.7951 (mttm) REVERT: B 342 GLN cc_start: 0.8015 (pp30) cc_final: 0.7703 (pp30) outliers start: 48 outliers final: 35 residues processed: 240 average time/residue: 0.0802 time to fit residues: 27.5382 Evaluate side-chains 227 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.0060 chunk 62 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.143023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113367 restraints weight = 19413.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116569 restraints weight = 11492.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118816 restraints weight = 8074.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120249 restraints weight = 6331.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121237 restraints weight = 5378.010| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9472 Z= 0.142 Angle : 0.869 14.085 12807 Z= 0.420 Chirality : 0.050 0.293 1449 Planarity : 0.005 0.065 1621 Dihedral : 8.127 78.930 1328 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.25 % Allowed : 27.73 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.86 (0.24), residues: 1142 helix: -1.11 (0.24), residues: 443 sheet: -2.54 (0.60), residues: 61 loop : -2.49 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 53 TYR 0.016 0.001 TYR B 239 PHE 0.027 0.002 PHE B 130 TRP 0.047 0.003 TRP A 379 HIS 0.008 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9469) covalent geometry : angle 0.86938 / 0.42 (12801) hydrogen bonds : bond 0.03720 / 2.37 ( 281) hydrogen bonds : angle 5.60397 / 4.02 ( 774) Misc. bond : bond 0.00029 / 0.02 ( 1) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.34492 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7857 (mm) REVERT: A 401 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8280 (tpt) REVERT: A 417 SER cc_start: 0.8971 (t) cc_final: 0.8639 (t) REVERT: A 425 TYR cc_start: 0.7006 (m-10) cc_final: 0.6772 (m-10) REVERT: A 431 ILE cc_start: 0.8201 (mt) cc_final: 0.7986 (mt) REVERT: A 525 GLN cc_start: 0.7429 (tm-30) cc_final: 0.6920 (pp30) REVERT: A 815 MET cc_start: 0.8022 (mtm) cc_final: 0.7751 (mtm) REVERT: A 832 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: C 196 LYS cc_start: 0.7274 (mttt) cc_final: 0.6989 (mmtm) REVERT: C 267 TYR cc_start: 0.7800 (t80) cc_final: 0.7486 (t80) REVERT: C 272 ARG cc_start: 0.6816 (ptm160) cc_final: 0.6447 (ptp-170) REVERT: C 361 GLU cc_start: 0.8326 (tt0) cc_final: 0.7857 (tm-30) REVERT: B 63 SER cc_start: 0.8135 (m) cc_final: 0.7872 (p) REVERT: B 114 MET cc_start: 0.7765 (tpp) cc_final: 0.7081 (mpp) REVERT: B 120 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7861 (t80) REVERT: B 164 VAL cc_start: 0.8990 (m) cc_final: 0.8655 (t) REVERT: B 166 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8672 (tm) REVERT: B 168 ILE cc_start: 0.9424 (pt) cc_final: 0.8839 (mt) REVERT: B 191 ASP cc_start: 0.8470 (p0) cc_final: 0.8245 (p0) REVERT: B 201 LYS cc_start: 0.8172 (mttt) cc_final: 0.7915 (mttm) REVERT: B 212 PHE cc_start: 0.8031 (m-80) cc_final: 0.7776 (m-10) REVERT: B 342 GLN cc_start: 0.8048 (pp30) cc_final: 0.7717 (pp30) outliers start: 44 outliers final: 35 residues processed: 239 average time/residue: 0.0837 time to fit residues: 28.4157 Evaluate side-chains 232 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 0.0670 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** 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 = 0.4048 r_free = 0.4048 target = 0.144200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114625 restraints weight = 19425.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.117959 restraints weight = 11536.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120194 restraints weight = 8067.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.121686 restraints weight = 6304.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122759 restraints weight = 5346.658| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9472 Z= 0.142 Angle : 0.883 14.234 12807 Z= 0.427 Chirality : 0.050 0.288 1449 Planarity : 0.005 0.065 1621 Dihedral : 8.031 78.996 1328 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 4.25 % Allowed : 28.21 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.88 (0.24), residues: 1142 helix: -1.10 (0.24), residues: 443 sheet: -2.43 (0.60), residues: 61 loop : -2.55 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 380 TYR 0.019 0.001 TYR B 105 PHE 0.029 0.002 PHE B 130 TRP 0.046 0.003 TRP B 22 HIS 0.010 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9469) covalent geometry : angle 0.88347 / 0.43 (12801) hydrogen bonds : bond 0.03666 / 2.34 ( 281) hydrogen bonds : angle 5.57849 / 4.01 ( 774) Misc. bond : bond 0.00034 / 0.02 ( 1) link_TRANS : bond 0.00097 / 0.05 ( 2) link_TRANS : angle 0.35326 / 0.19 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7713 (pp20) cc_final: 0.7460 (pp20) REVERT: A 317 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7816 (mm) REVERT: A 401 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8284 (tpt) REVERT: A 416 LYS cc_start: 0.7825 (tmmm) cc_final: 0.7588 (tttp) REVERT: A 417 SER cc_start: 0.8995 (t) cc_final: 0.8685 (t) REVERT: A 431 ILE cc_start: 0.8183 (mt) cc_final: 0.7979 (mt) REVERT: A 525 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6848 (pp30) REVERT: A 546 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7284 (mmmt) REVERT: A 701 GLU cc_start: 0.7957 (mp0) cc_final: 0.7406 (pp20) REVERT: A 815 MET cc_start: 0.8020 (mtm) cc_final: 0.7754 (mtm) REVERT: A 832 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: C 196 LYS cc_start: 0.7271 (mttt) cc_final: 0.6959 (mmtm) REVERT: C 267 TYR cc_start: 0.7871 (t80) cc_final: 0.7466 (t80) REVERT: C 272 ARG cc_start: 0.6728 (ptm160) cc_final: 0.6419 (ptp-170) REVERT: C 361 GLU cc_start: 0.8332 (tt0) cc_final: 0.7871 (tm-30) REVERT: B 114 MET cc_start: 0.7743 (tpp) cc_final: 0.7042 (mpp) REVERT: B 120 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7928 (t80) REVERT: B 164 VAL cc_start: 0.9022 (m) cc_final: 0.8663 (t) REVERT: B 166 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8707 (tm) REVERT: B 168 ILE cc_start: 0.9454 (pt) cc_final: 0.8909 (mt) REVERT: B 191 ASP cc_start: 0.8387 (p0) cc_final: 0.8153 (p0) REVERT: B 342 GLN cc_start: 0.8064 (pp30) cc_final: 0.7745 (pp30) outliers start: 44 outliers final: 37 residues processed: 239 average time/residue: 0.0861 time to fit residues: 29.3628 Evaluate side-chains 233 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.145595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116220 restraints weight = 19396.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119592 restraints weight = 11550.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121888 restraints weight = 8061.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.123401 restraints weight = 6298.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.124283 restraints weight = 5321.452| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9472 Z= 0.146 Angle : 0.894 13.888 12807 Z= 0.433 Chirality : 0.050 0.288 1449 Planarity : 0.005 0.077 1621 Dihedral : 7.936 79.050 1328 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 4.06 % Allowed : 28.50 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.79 (0.24), residues: 1142 helix: -1.06 (0.24), residues: 444 sheet: -2.40 (0.61), residues: 61 loop : -2.46 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 293 TYR 0.019 0.001 TYR B 105 PHE 0.029 0.002 PHE B 212 TRP 0.039 0.003 TRP B 22 HIS 0.010 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9469) covalent geometry : angle 0.89463 / 0.43 (12801) hydrogen bonds : bond 0.03652 / 2.31 ( 281) hydrogen bonds : angle 5.57679 / 4.01 ( 774) Misc. bond : bond 0.00045 / 0.02 ( 1) link_TRANS : bond 0.00091 / 0.05 ( 2) link_TRANS : angle 0.38383 / 0.20 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.98 seconds wall clock time: 29 minutes 4.28 seconds (1744.28 seconds total)