Starting phenix.real_space_refine on Sat Sep 12 00:26:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kup_9579/09_2026/6kup_9579_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kup_9579/09_2026/6kup_9579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kup_9579/09_2026/6kup_9579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kup_9579/09_2026/6kup_9579.map" model { file = "/net/cci-nas-00/data/ceres_data/6kup_9579/09_2026/6kup_9579_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kup_9579/09_2026/6kup_9579_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 109 5.16 5 C 7703 2.51 5 N 2092 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 12254 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5578 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 2.79, per 1000 atoms: 0.23 Number of scatterers: 12254 At special positions: 0 Unit cell: (111.52, 110.16, 110.16, 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 109 16.00 P 23 15.00 O 2327 8.00 N 2092 7.00 C 7703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 415.7 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 48.0% alpha, 7.7% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.743A pdb=" N ALA A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.720A pdb=" N THR A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.100A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.749A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 4.049A pdb=" N ASP A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 589 removed outlier: 4.136A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.591A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.799A pdb=" N CYS A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.700A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.796A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.997A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.618A pdb=" N GLU B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.645A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.534A pdb=" N CYS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.772A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.873A pdb=" N CYS B 314 " --> pdb=" O TRP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 4.042A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.549A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.677A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.646A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 560 removed outlier: 3.512A pdb=" N ALA B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.831A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.577A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.573A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.989A pdb=" N LEU B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.739A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 30 through 37 removed outlier: 3.964A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.553A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.529A pdb=" N THR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.730A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.601A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.674A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.863A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.604A pdb=" N MET C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.830A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.724A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 478 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.561A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA9, first strand: chain 'B' and resid 438 through 443 removed outlier: 4.133A pdb=" N PHE B 448 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AB3, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.723A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 153 512 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.13 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: 1.22 - 1.34: 3691 1.34 - 1.46: 2351 1.46 - 1.58: 6278 1.58 - 1.70: 44 1.70 - 1.82: 181 Bond restraints: 12545 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.27e-02 6.20e+03 2.11e+01 bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.371 -0.037 8.40e-03 1.42e+04 1.98e+01 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.426 0.033 1.25e-02 6.40e+03 6.81e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.428 0.031 1.25e-02 6.40e+03 5.96e+00 bond pdb=" C LEU A 203 " pdb=" N PRO A 204 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 ... (remaining 12540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 16094 1.65 - 3.30: 719 3.30 - 4.95: 112 4.95 - 6.60: 23 6.60 - 8.25: 14 Bond angle restraints: 16962 Sorted by residual: angle pdb=" C LEU B 540 " pdb=" N SER B 541 " pdb=" CA SER B 541 " ideal model delta sigma weight residual 120.51 127.61 -7.10 1.45e+00 4.76e-01 2.40e+01 angle pdb=" N1 U R 2 " pdb=" C6 U R 2 " pdb=" C5 U R 2 " ideal model delta sigma weight residual 122.70 125.14 -2.44 5.00e-01 4.00e+00 2.39e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 111.90 -3.70 8.00e-01 1.56e+00 2.14e+01 angle pdb=" O5' A V 7 " pdb=" C5' A V 7 " pdb=" C4' A V 7 " ideal model delta sigma weight residual 109.40 112.99 -3.59 8.00e-01 1.56e+00 2.01e+01 angle pdb=" O5' U R 5 " pdb=" C5' U R 5 " pdb=" C4' U R 5 " ideal model delta sigma weight residual 109.40 112.85 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 16957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 7253 15.20 - 30.40: 309 30.40 - 45.60: 102 45.60 - 60.80: 29 60.80 - 76.01: 27 Dihedral angle restraints: 7720 sinusoidal: 3460 harmonic: 4260 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA THR B 328 " pdb=" C THR B 328 " pdb=" N LYS B 329 " pdb=" CA LYS B 329 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1389 0.054 - 0.109: 375 0.109 - 0.163: 82 0.163 - 0.217: 6 0.217 - 0.272: 3 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CB ILE B 304 " pdb=" CA ILE B 304 " pdb=" CG1 ILE B 304 " pdb=" CG2 ILE B 304 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE C 231 " pdb=" CA ILE C 231 " pdb=" CG1 ILE C 231 " pdb=" CG2 ILE C 231 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1852 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 155 " -0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO C 156 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 342 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO B 343 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 731 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C ILE B 731 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE B 731 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1933 2.76 - 3.30: 11010 3.30 - 3.83: 19001 3.83 - 4.37: 22663 4.37 - 4.90: 38410 Nonbonded interactions: 93017 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.227 3.120 nonbonded pdb=" O LEU B 324 " pdb=" OG1 THR B 328 " model vdw 2.296 3.040 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.297 3.040 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.308 3.040 nonbonded pdb=" O VAL B 341 " pdb=" OG1 THR B 344 " model vdw 2.313 3.040 ... (remaining 93012 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.600 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.004 0.058 12545 Z= 0.215 Angle : 0.821 8.248 16962 Z= 0.496 Chirality : 0.051 0.272 1855 Planarity : 0.006 0.069 2070 Dihedral : 11.438 76.006 4954 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % 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: -4.90 (0.16), residues: 1441 helix: -3.42 (0.12), residues: 647 sheet: -1.84 (0.52), residues: 91 loop : -3.28 (0.19), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 438 TYR 0.018 0.002 TYR A 549 PHE 0.026 0.002 PHE B 726 TRP 0.029 0.003 TRP A 386 HIS 0.007 0.002 HIS B 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.22 (12545) covalent geometry : angle 0.82119 / 0.50 (16962) hydrogen bonds : bond 0.14526 / 9.96 ( 531) hydrogen bonds : angle 9.05112 / 6.16 ( 1457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 566 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 TRP cc_start: 0.7767 (t-100) cc_final: 0.7096 (t-100) REVERT: A 278 ASP cc_start: 0.8685 (t0) cc_final: 0.8424 (t0) REVERT: A 288 LEU cc_start: 0.9683 (tp) cc_final: 0.9461 (tt) REVERT: A 332 GLU cc_start: 0.7990 (tt0) cc_final: 0.7661 (pt0) REVERT: A 364 GLU cc_start: 0.8341 (mp0) cc_final: 0.8052 (mp0) REVERT: A 382 PHE cc_start: 0.7765 (t80) cc_final: 0.7122 (t80) REVERT: A 386 TRP cc_start: 0.8882 (t-100) cc_final: 0.8254 (t-100) REVERT: A 453 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7674 (tp30) REVERT: A 495 ASP cc_start: 0.8666 (m-30) cc_final: 0.8166 (m-30) REVERT: A 498 TYR cc_start: 0.8407 (p90) cc_final: 0.8100 (p90) REVERT: A 547 PHE cc_start: 0.9005 (m-80) cc_final: 0.8558 (m-10) REVERT: A 555 MET cc_start: 0.8238 (mmm) cc_final: 0.7768 (mmm) REVERT: A 562 TRP cc_start: 0.7924 (m100) cc_final: 0.7206 (m100) REVERT: A 578 GLU cc_start: 0.8803 (tt0) cc_final: 0.8426 (tt0) REVERT: A 600 LYS cc_start: 0.9278 (tppt) cc_final: 0.8777 (tptp) REVERT: A 601 ARG cc_start: 0.8753 (mmt180) cc_final: 0.8530 (mmm160) REVERT: A 639 ASP cc_start: 0.7436 (m-30) cc_final: 0.6539 (m-30) REVERT: A 650 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8329 (mtmt) REVERT: A 661 ASP cc_start: 0.7648 (t0) cc_final: 0.7440 (t0) REVERT: A 684 ASN cc_start: 0.9318 (t0) cc_final: 0.9100 (t0) REVERT: B 10 LEU cc_start: 0.9528 (mt) cc_final: 0.9275 (tt) REVERT: B 45 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.8004 (ttp-170) REVERT: B 52 THR cc_start: 0.8465 (t) cc_final: 0.8184 (t) REVERT: B 85 VAL cc_start: 0.9349 (t) cc_final: 0.8882 (t) REVERT: B 147 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8246 (mm-40) REVERT: B 151 ASP cc_start: 0.8473 (t0) cc_final: 0.7641 (t70) REVERT: B 155 GLU cc_start: 0.7725 (tt0) cc_final: 0.7412 (pt0) REVERT: B 182 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7681 (mtmm) REVERT: B 234 GLU cc_start: 0.7109 (tt0) cc_final: 0.6434 (pm20) REVERT: B 237 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8286 (mptt) REVERT: B 255 LYS cc_start: 0.8564 (tptt) cc_final: 0.8185 (tptt) REVERT: B 311 TRP cc_start: 0.9365 (t-100) cc_final: 0.9085 (t-100) REVERT: B 336 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8429 (mmtp) REVERT: B 389 LEU cc_start: 0.9390 (mt) cc_final: 0.9165 (tp) REVERT: B 410 MET cc_start: 0.5922 (mtp) cc_final: 0.5688 (mtt) REVERT: B 541 SER cc_start: 0.8831 (p) cc_final: 0.8034 (p) REVERT: B 576 ILE cc_start: 0.9376 (mt) cc_final: 0.8946 (tp) REVERT: B 578 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7005 (ptm-80) REVERT: B 610 GLU cc_start: 0.8754 (mp0) cc_final: 0.7889 (pm20) REVERT: B 612 LEU cc_start: 0.8521 (tp) cc_final: 0.7930 (tp) REVERT: B 627 ASN cc_start: 0.8756 (t0) cc_final: 0.8426 (t0) REVERT: B 689 CYS cc_start: 0.8548 (m) cc_final: 0.8255 (m) REVERT: B 736 TYR cc_start: 0.8102 (t80) cc_final: 0.6475 (t80) REVERT: C 55 MET cc_start: 0.8368 (mmm) cc_final: 0.8089 (mmm) REVERT: C 85 LYS cc_start: 0.5817 (mmtm) cc_final: 0.4828 (ptpt) REVERT: C 96 LEU cc_start: 0.8227 (mt) cc_final: 0.7923 (mt) REVERT: C 102 ILE cc_start: 0.8970 (mt) cc_final: 0.8580 (mm) REVERT: C 213 MET cc_start: 0.8486 (ptm) cc_final: 0.8167 (ppp) REVERT: C 218 PHE cc_start: 0.7928 (m-10) cc_final: 0.6824 (m-80) REVERT: C 247 TRP cc_start: 0.8394 (p-90) cc_final: 0.7656 (p90) outliers start: 2 outliers final: 0 residues processed: 566 average time/residue: 0.1304 time to fit residues: 101.6058 Evaluate side-chains 357 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 HIS A 277 HIS A 560 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN B 70 ASN B 147 GLN B 477 ASN B 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109466 restraints weight = 27560.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112796 restraints weight = 15971.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115119 restraints weight = 10734.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116694 restraints weight = 7979.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117591 restraints weight = 6441.837| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 12545 Z= 0.171 Angle : 0.705 13.574 16962 Z= 0.366 Chirality : 0.044 0.184 1855 Planarity : 0.006 0.062 2070 Dihedral : 11.752 74.975 1924 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: -3.30 (0.19), residues: 1441 helix: -1.46 (0.18), residues: 651 sheet: -1.92 (0.50), residues: 98 loop : -2.99 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 592 TYR 0.033 0.002 TYR B 736 PHE 0.025 0.002 PHE B 108 TRP 0.019 0.002 TRP A 386 HIS 0.008 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (12545) covalent geometry : angle 0.70475 / 0.37 (16962) hydrogen bonds : bond 0.05422 / 3.67 ( 531) hydrogen bonds : angle 5.94971 / 4.08 ( 1457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 TRP cc_start: 0.7486 (t-100) cc_final: 0.7010 (t-100) REVERT: A 288 LEU cc_start: 0.9660 (tp) cc_final: 0.9391 (tt) REVERT: A 315 TYR cc_start: 0.8138 (m-80) cc_final: 0.7782 (m-80) REVERT: A 382 PHE cc_start: 0.7480 (t80) cc_final: 0.6656 (t80) REVERT: A 386 TRP cc_start: 0.8877 (t-100) cc_final: 0.7940 (t-100) REVERT: A 453 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7444 (tp30) REVERT: A 546 LEU cc_start: 0.9331 (tp) cc_final: 0.9058 (tt) REVERT: A 547 PHE cc_start: 0.8928 (m-80) cc_final: 0.8315 (m-10) REVERT: A 555 MET cc_start: 0.8486 (mmm) cc_final: 0.8255 (mmm) REVERT: A 639 ASP cc_start: 0.6945 (m-30) cc_final: 0.6730 (m-30) REVERT: A 650 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8359 (ptpt) REVERT: A 654 MET cc_start: 0.8511 (tpp) cc_final: 0.8203 (tpp) REVERT: A 684 ASN cc_start: 0.9282 (t0) cc_final: 0.9001 (t0) REVERT: B 2 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7032 (mt-10) REVERT: B 10 LEU cc_start: 0.9520 (mt) cc_final: 0.9315 (tt) REVERT: B 49 TYR cc_start: 0.8340 (m-10) cc_final: 0.8116 (m-10) REVERT: B 52 THR cc_start: 0.8404 (t) cc_final: 0.8140 (t) REVERT: B 78 LEU cc_start: 0.8887 (tp) cc_final: 0.8589 (tp) REVERT: B 92 SER cc_start: 0.9280 (m) cc_final: 0.9024 (p) REVERT: B 112 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8274 (mp0) REVERT: B 151 ASP cc_start: 0.8556 (t0) cc_final: 0.7775 (t70) REVERT: B 174 GLU cc_start: 0.8507 (tt0) cc_final: 0.7858 (tt0) REVERT: B 175 MET cc_start: 0.9128 (ptp) cc_final: 0.8782 (ptt) REVERT: B 234 GLU cc_start: 0.7057 (tt0) cc_final: 0.6497 (pm20) REVERT: B 237 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8487 (mptt) REVERT: B 255 LYS cc_start: 0.8720 (tptt) cc_final: 0.8372 (tptt) REVERT: B 262 GLN cc_start: 0.8169 (tt0) cc_final: 0.7340 (tm-30) REVERT: B 312 ASN cc_start: 0.8932 (m-40) cc_final: 0.8412 (m-40) REVERT: B 328 THR cc_start: 0.7839 (p) cc_final: 0.7423 (p) REVERT: B 408 MET cc_start: 0.6536 (ttm) cc_final: 0.5809 (ttp) REVERT: B 490 LEU cc_start: 0.9018 (tp) cc_final: 0.8601 (tp) REVERT: B 496 MET cc_start: 0.8644 (mtm) cc_final: 0.8033 (mtt) REVERT: B 528 MET cc_start: 0.8847 (mtm) cc_final: 0.8484 (mtp) REVERT: B 574 MET cc_start: 0.8328 (mmm) cc_final: 0.8054 (tpp) REVERT: B 578 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7467 (mtp180) REVERT: B 587 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7882 (mmmt) REVERT: B 591 LEU cc_start: 0.9161 (tp) cc_final: 0.8816 (tp) REVERT: B 602 ILE cc_start: 0.8973 (mm) cc_final: 0.8702 (pt) REVERT: B 612 LEU cc_start: 0.8346 (tp) cc_final: 0.8083 (tp) REVERT: C 85 LYS cc_start: 0.5651 (mmtm) cc_final: 0.4479 (ptpt) REVERT: C 157 VAL cc_start: 0.6867 (t) cc_final: 0.6630 (p) REVERT: C 213 MET cc_start: 0.9137 (ptm) cc_final: 0.8534 (ppp) REVERT: C 214 ILE cc_start: 0.9340 (mt) cc_final: 0.8922 (mt) REVERT: C 217 GLN cc_start: 0.8577 (pm20) cc_final: 0.8099 (pm20) REVERT: C 218 PHE cc_start: 0.8349 (m-10) cc_final: 0.7087 (m-80) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.1187 time to fit residues: 68.4410 Evaluate side-chains 336 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN B 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107374 restraints weight = 27244.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110591 restraints weight = 15463.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112817 restraints weight = 10223.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114324 restraints weight = 7540.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115421 restraints weight = 6059.682| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12545 Z= 0.160 Angle : 0.656 11.839 16962 Z= 0.343 Chirality : 0.043 0.180 1855 Planarity : 0.006 0.124 2070 Dihedral : 11.599 74.593 1924 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 0.23 % Allowed : 2.33 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.20), residues: 1441 helix: -0.54 (0.19), residues: 655 sheet: -1.82 (0.49), residues: 103 loop : -2.78 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 455 TYR 0.020 0.002 TYR B 736 PHE 0.022 0.001 PHE B 108 TRP 0.016 0.002 TRP C 53 HIS 0.012 0.002 HIS B 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (12545) covalent geometry : angle 0.65598 / 0.34 (16962) hydrogen bonds : bond 0.04995 / 3.34 ( 531) hydrogen bonds : angle 5.25307 / 3.62 ( 1457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.6898 (tpm170) cc_final: 0.6330 (tpm170) REVERT: A 271 TRP cc_start: 0.7523 (t-100) cc_final: 0.7026 (t-100) REVERT: A 292 PHE cc_start: 0.7433 (t80) cc_final: 0.7145 (t80) REVERT: A 340 ASP cc_start: 0.8601 (t0) cc_final: 0.8292 (t70) REVERT: A 382 PHE cc_start: 0.7612 (t80) cc_final: 0.6762 (t80) REVERT: A 386 TRP cc_start: 0.8841 (t-100) cc_final: 0.7803 (t-100) REVERT: A 390 MET cc_start: 0.8626 (ptm) cc_final: 0.8192 (ttm) REVERT: A 453 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7658 (tp30) REVERT: A 546 LEU cc_start: 0.9332 (tp) cc_final: 0.9078 (tt) REVERT: A 547 PHE cc_start: 0.8867 (m-80) cc_final: 0.8208 (m-10) REVERT: A 649 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 653 LEU cc_start: 0.9408 (mp) cc_final: 0.9058 (mp) REVERT: A 654 MET cc_start: 0.8599 (tpp) cc_final: 0.8113 (tpp) REVERT: A 684 ASN cc_start: 0.9236 (t0) cc_final: 0.9023 (t0) REVERT: A 692 ASP cc_start: 0.8482 (t0) cc_final: 0.8196 (t0) REVERT: A 698 PHE cc_start: 0.9244 (m-10) cc_final: 0.9043 (m-10) REVERT: A 708 TYR cc_start: 0.8448 (m-80) cc_final: 0.7862 (m-80) REVERT: B 2 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6748 (mp0) REVERT: B 45 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7937 (mtm180) REVERT: B 52 THR cc_start: 0.8423 (t) cc_final: 0.8147 (t) REVERT: B 78 LEU cc_start: 0.8906 (tp) cc_final: 0.7626 (tp) REVERT: B 90 MET cc_start: 0.9103 (ptm) cc_final: 0.8621 (ptm) REVERT: B 112 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 140 MET cc_start: 0.7796 (tpp) cc_final: 0.7154 (ttp) REVERT: B 174 GLU cc_start: 0.8575 (tt0) cc_final: 0.7869 (tt0) REVERT: B 175 MET cc_start: 0.9148 (ptp) cc_final: 0.8716 (ptt) REVERT: B 183 PHE cc_start: 0.8736 (p90) cc_final: 0.7954 (p90) REVERT: B 234 GLU cc_start: 0.7062 (tt0) cc_final: 0.6723 (pm20) REVERT: B 237 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8381 (mptt) REVERT: B 255 LYS cc_start: 0.8777 (tptt) cc_final: 0.8271 (tptt) REVERT: B 258 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7113 (mt-10) REVERT: B 262 GLN cc_start: 0.8400 (tt0) cc_final: 0.7226 (tm-30) REVERT: B 266 GLU cc_start: 0.8251 (mt-10) cc_final: 0.5565 (mt-10) REVERT: B 312 ASN cc_start: 0.8857 (m110) cc_final: 0.8368 (m-40) REVERT: B 320 TYR cc_start: 0.8600 (m-10) cc_final: 0.8370 (m-10) REVERT: B 408 MET cc_start: 0.6709 (ttm) cc_final: 0.5951 (ttp) REVERT: B 460 MET cc_start: 0.8391 (tpp) cc_final: 0.8087 (tpp) REVERT: B 461 GLU cc_start: 0.8262 (pt0) cc_final: 0.8001 (pt0) REVERT: B 490 LEU cc_start: 0.9092 (tp) cc_final: 0.8636 (tp) REVERT: B 492 GLU cc_start: 0.8081 (tt0) cc_final: 0.7817 (tm-30) REVERT: B 496 MET cc_start: 0.8612 (mtm) cc_final: 0.8272 (mtt) REVERT: B 528 MET cc_start: 0.8956 (mtm) cc_final: 0.8568 (mtp) REVERT: B 574 MET cc_start: 0.8326 (mmm) cc_final: 0.8021 (tpp) REVERT: B 578 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7402 (mtm180) REVERT: B 587 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7902 (tppt) REVERT: B 591 LEU cc_start: 0.9213 (tp) cc_final: 0.8926 (tp) REVERT: B 681 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 749 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 55 MET cc_start: 0.8364 (mmm) cc_final: 0.7918 (mmm) REVERT: C 75 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7465 (pm20) REVERT: C 102 ILE cc_start: 0.8930 (mt) cc_final: 0.8719 (mp) REVERT: C 130 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 157 VAL cc_start: 0.6969 (t) cc_final: 0.6701 (p) REVERT: C 171 MET cc_start: 0.8242 (mmt) cc_final: 0.7995 (mmt) REVERT: C 213 MET cc_start: 0.9143 (ptm) cc_final: 0.8738 (ppp) REVERT: C 218 PHE cc_start: 0.8244 (m-10) cc_final: 0.7031 (m-80) outliers start: 3 outliers final: 0 residues processed: 387 average time/residue: 0.1158 time to fit residues: 63.8135 Evaluate side-chains 321 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 chunk 50 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN B 660 HIS C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106867 restraints weight = 27334.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110081 restraints weight = 15819.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112302 restraints weight = 10587.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113840 restraints weight = 7886.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114866 restraints weight = 6359.234| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12545 Z= 0.143 Angle : 0.623 11.899 16962 Z= 0.327 Chirality : 0.043 0.188 1855 Planarity : 0.004 0.052 2070 Dihedral : 11.468 74.418 1924 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 0.16 % Allowed : 2.33 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.21), residues: 1441 helix: -0.12 (0.20), residues: 657 sheet: -1.57 (0.52), residues: 98 loop : -2.65 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 625 TYR 0.018 0.002 TYR B 736 PHE 0.041 0.002 PHE B 183 TRP 0.013 0.001 TRP A 386 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12545) covalent geometry : angle 0.62334 / 0.33 (16962) hydrogen bonds : bond 0.04706 / 3.15 ( 531) hydrogen bonds : angle 4.99889 / 3.48 ( 1457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ILE cc_start: 0.9325 (mt) cc_final: 0.8673 (tt) REVERT: A 271 TRP cc_start: 0.7503 (t-100) cc_final: 0.7040 (t-100) REVERT: A 292 PHE cc_start: 0.7447 (t80) cc_final: 0.7152 (t80) REVERT: A 340 ASP cc_start: 0.8648 (t0) cc_final: 0.8289 (t70) REVERT: A 390 MET cc_start: 0.8484 (ptm) cc_final: 0.8166 (ttm) REVERT: A 442 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8160 (mmmm) REVERT: A 453 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7743 (tp30) REVERT: A 546 LEU cc_start: 0.9349 (tp) cc_final: 0.9069 (tt) REVERT: A 547 PHE cc_start: 0.8818 (m-80) cc_final: 0.8156 (m-10) REVERT: A 639 ASP cc_start: 0.8456 (t0) cc_final: 0.6918 (m-30) REVERT: A 643 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7498 (mm-30) REVERT: A 653 LEU cc_start: 0.9449 (mp) cc_final: 0.9199 (mp) REVERT: A 654 MET cc_start: 0.8532 (tpp) cc_final: 0.8227 (tpp) REVERT: A 684 ASN cc_start: 0.9167 (t0) cc_final: 0.8783 (t0) REVERT: A 692 ASP cc_start: 0.8510 (t0) cc_final: 0.8063 (t0) REVERT: B 2 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6748 (mp0) REVERT: B 45 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7672 (mtm180) REVERT: B 52 THR cc_start: 0.8443 (t) cc_final: 0.8147 (t) REVERT: B 78 LEU cc_start: 0.8796 (tp) cc_final: 0.8360 (tp) REVERT: B 133 ASP cc_start: 0.8105 (t70) cc_final: 0.7609 (m-30) REVERT: B 138 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.7214 (ttp-110) REVERT: B 174 GLU cc_start: 0.8609 (tt0) cc_final: 0.7859 (tt0) REVERT: B 175 MET cc_start: 0.9004 (ptp) cc_final: 0.8588 (ptt) REVERT: B 234 GLU cc_start: 0.7008 (tt0) cc_final: 0.6692 (pm20) REVERT: B 237 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8394 (mptt) REVERT: B 255 LYS cc_start: 0.8802 (tptt) cc_final: 0.8154 (tptt) REVERT: B 258 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 262 GLN cc_start: 0.8481 (tt0) cc_final: 0.7300 (tm-30) REVERT: B 266 GLU cc_start: 0.8261 (mt-10) cc_final: 0.5426 (mt-10) REVERT: B 312 ASN cc_start: 0.8885 (m110) cc_final: 0.8355 (m-40) REVERT: B 320 TYR cc_start: 0.8752 (m-10) cc_final: 0.8550 (m-10) REVERT: B 375 MET cc_start: 0.8916 (mtp) cc_final: 0.8604 (mtp) REVERT: B 402 CYS cc_start: 0.8589 (t) cc_final: 0.8169 (t) REVERT: B 408 MET cc_start: 0.6731 (ttm) cc_final: 0.5956 (ttp) REVERT: B 423 MET cc_start: 0.9691 (mtp) cc_final: 0.9473 (mtp) REVERT: B 460 MET cc_start: 0.8357 (tpp) cc_final: 0.8075 (tpp) REVERT: B 490 LEU cc_start: 0.9073 (tp) cc_final: 0.8633 (tp) REVERT: B 492 GLU cc_start: 0.8164 (tt0) cc_final: 0.7800 (tm-30) REVERT: B 496 MET cc_start: 0.8593 (mtm) cc_final: 0.8281 (mtt) REVERT: B 528 MET cc_start: 0.8994 (mtm) cc_final: 0.8789 (mtp) REVERT: B 547 MET cc_start: 0.9140 (tpp) cc_final: 0.8643 (ttm) REVERT: B 574 MET cc_start: 0.8332 (mmm) cc_final: 0.7981 (tpp) REVERT: B 587 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7969 (mmmt) REVERT: B 681 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7547 (mm-30) REVERT: B 740 LYS cc_start: 0.8869 (mttt) cc_final: 0.8523 (mmtt) REVERT: B 749 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7090 (tm-30) REVERT: C 55 MET cc_start: 0.8354 (mmm) cc_final: 0.7959 (mmm) REVERT: C 85 LYS cc_start: 0.5445 (mmmm) cc_final: 0.3867 (ptpt) REVERT: C 102 ILE cc_start: 0.8976 (mt) cc_final: 0.8745 (mp) REVERT: C 123 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8237 (mmmt) REVERT: C 157 VAL cc_start: 0.7114 (t) cc_final: 0.6857 (p) REVERT: C 171 MET cc_start: 0.8125 (mmt) cc_final: 0.7882 (mmt) REVERT: C 213 MET cc_start: 0.9125 (ptm) cc_final: 0.8531 (ppp) REVERT: C 218 PHE cc_start: 0.8242 (m-10) cc_final: 0.7129 (m-80) outliers start: 2 outliers final: 0 residues processed: 382 average time/residue: 0.1188 time to fit residues: 64.4547 Evaluate side-chains 301 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 141 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 125 optimal weight: 0.0050 chunk 39 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN B 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107672 restraints weight = 27247.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110697 restraints weight = 16099.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112789 restraints weight = 10927.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114296 restraints weight = 8228.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115255 restraints weight = 6661.105| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12545 Z= 0.135 Angle : 0.612 10.807 16962 Z= 0.317 Chirality : 0.042 0.185 1855 Planarity : 0.004 0.046 2070 Dihedral : 11.374 74.263 1924 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 0.08 % Allowed : 2.33 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1441 helix: 0.18 (0.20), residues: 660 sheet: -1.50 (0.49), residues: 118 loop : -2.58 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 131 TYR 0.015 0.002 TYR C 104 PHE 0.025 0.001 PHE B 183 TRP 0.011 0.001 TRP A 386 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12545) covalent geometry : angle 0.61177 / 0.32 (16962) hydrogen bonds : bond 0.04469 / 2.99 ( 531) hydrogen bonds : angle 4.82952 / 3.39 ( 1457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ILE cc_start: 0.9378 (mt) cc_final: 0.8851 (tt) REVERT: A 271 TRP cc_start: 0.7587 (t-100) cc_final: 0.7110 (t-100) REVERT: A 340 ASP cc_start: 0.8669 (t0) cc_final: 0.8262 (t70) REVERT: A 390 MET cc_start: 0.8457 (ptm) cc_final: 0.8227 (ttm) REVERT: A 406 MET cc_start: 0.6759 (ttm) cc_final: 0.5758 (ttp) REVERT: A 442 LYS cc_start: 0.8820 (mttm) cc_final: 0.8602 (mttp) REVERT: A 453 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7565 (tp30) REVERT: A 546 LEU cc_start: 0.9381 (tp) cc_final: 0.9162 (tt) REVERT: A 547 PHE cc_start: 0.8841 (m-80) cc_final: 0.8081 (m-10) REVERT: A 639 ASP cc_start: 0.8571 (t70) cc_final: 0.6817 (m-30) REVERT: A 643 GLU cc_start: 0.8666 (mt-10) cc_final: 0.7463 (mm-30) REVERT: A 654 MET cc_start: 0.8510 (tpp) cc_final: 0.8120 (tpp) REVERT: A 684 ASN cc_start: 0.9148 (t0) cc_final: 0.8773 (t0) REVERT: B 4 ASN cc_start: 0.9409 (t0) cc_final: 0.8757 (t0) REVERT: B 7 LEU cc_start: 0.9635 (mt) cc_final: 0.9403 (mt) REVERT: B 52 THR cc_start: 0.8448 (t) cc_final: 0.8134 (t) REVERT: B 78 LEU cc_start: 0.8639 (tp) cc_final: 0.8347 (tp) REVERT: B 80 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9001 (mmtm) REVERT: B 85 VAL cc_start: 0.9219 (t) cc_final: 0.9004 (t) REVERT: B 87 ILE cc_start: 0.9411 (pt) cc_final: 0.9024 (mp) REVERT: B 112 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8234 (mp0) REVERT: B 114 GLU cc_start: 0.6819 (pp20) cc_final: 0.6520 (pp20) REVERT: B 133 ASP cc_start: 0.8246 (t70) cc_final: 0.7712 (m-30) REVERT: B 174 GLU cc_start: 0.8660 (tt0) cc_final: 0.8020 (tt0) REVERT: B 237 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8497 (mptt) REVERT: B 250 ILE cc_start: 0.8496 (mp) cc_final: 0.8275 (mp) REVERT: B 255 LYS cc_start: 0.8800 (tptt) cc_final: 0.7945 (tppt) REVERT: B 258 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6876 (mt-10) REVERT: B 262 GLN cc_start: 0.8477 (tt0) cc_final: 0.7295 (tm-30) REVERT: B 266 GLU cc_start: 0.8311 (mt-10) cc_final: 0.5550 (mt-10) REVERT: B 312 ASN cc_start: 0.8936 (m110) cc_final: 0.8323 (m-40) REVERT: B 320 TYR cc_start: 0.8658 (m-10) cc_final: 0.8368 (m-10) REVERT: B 375 MET cc_start: 0.8826 (mtp) cc_final: 0.8486 (mtp) REVERT: B 402 CYS cc_start: 0.8416 (t) cc_final: 0.8061 (t) REVERT: B 408 MET cc_start: 0.6861 (ttm) cc_final: 0.6067 (ttp) REVERT: B 423 MET cc_start: 0.9685 (mtp) cc_final: 0.9426 (mtp) REVERT: B 442 LEU cc_start: 0.8681 (tp) cc_final: 0.8078 (tp) REVERT: B 460 MET cc_start: 0.8461 (tpp) cc_final: 0.8231 (tpp) REVERT: B 490 LEU cc_start: 0.9062 (tp) cc_final: 0.8669 (tp) REVERT: B 496 MET cc_start: 0.8578 (mtm) cc_final: 0.8330 (mtt) REVERT: B 528 MET cc_start: 0.9066 (mtm) cc_final: 0.8836 (mtp) REVERT: B 574 MET cc_start: 0.8328 (mmm) cc_final: 0.7970 (tpp) REVERT: B 587 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8022 (mmmt) REVERT: B 599 MET cc_start: 0.8648 (tpp) cc_final: 0.8064 (tpt) REVERT: B 681 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 685 TYR cc_start: 0.7260 (m-10) cc_final: 0.6212 (m-80) REVERT: B 740 LYS cc_start: 0.8951 (mttt) cc_final: 0.8603 (mttm) REVERT: C 55 MET cc_start: 0.8366 (mmm) cc_final: 0.7882 (mmm) REVERT: C 81 ASP cc_start: 0.7684 (t0) cc_final: 0.7331 (t0) REVERT: C 102 ILE cc_start: 0.8979 (mt) cc_final: 0.8757 (mp) REVERT: C 123 LYS cc_start: 0.8560 (mmmt) cc_final: 0.7985 (mmmt) REVERT: C 170 THR cc_start: 0.7697 (p) cc_final: 0.6619 (p) REVERT: C 171 MET cc_start: 0.8228 (mmt) cc_final: 0.7869 (mmt) REVERT: C 213 MET cc_start: 0.9097 (ptm) cc_final: 0.8340 (ppp) REVERT: C 218 PHE cc_start: 0.8327 (m-10) cc_final: 0.7257 (m-80) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.1117 time to fit residues: 59.1925 Evaluate side-chains 298 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105843 restraints weight = 27751.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109070 restraints weight = 16099.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111192 restraints weight = 10822.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112734 restraints weight = 8157.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113795 restraints weight = 6619.833| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12545 Z= 0.150 Angle : 0.628 9.999 16962 Z= 0.325 Chirality : 0.043 0.216 1855 Planarity : 0.005 0.069 2070 Dihedral : 11.341 74.232 1924 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1441 helix: 0.27 (0.20), residues: 664 sheet: -1.51 (0.50), residues: 115 loop : -2.56 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 45 TYR 0.018 0.002 TYR B 6 PHE 0.023 0.001 PHE B 183 TRP 0.012 0.001 TRP C 83 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12545) covalent geometry : angle 0.62759 / 0.33 (16962) hydrogen bonds : bond 0.04456 / 2.97 ( 531) hydrogen bonds : angle 4.81070 / 3.39 ( 1457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.6741 (tpm170) cc_final: 0.6504 (mmm160) REVERT: A 253 ILE cc_start: 0.9376 (mt) cc_final: 0.8889 (tt) REVERT: A 340 ASP cc_start: 0.8653 (t0) cc_final: 0.8286 (t70) REVERT: A 406 MET cc_start: 0.6749 (ttm) cc_final: 0.5676 (ttp) REVERT: A 453 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7552 (tp30) REVERT: A 546 LEU cc_start: 0.9350 (tp) cc_final: 0.9123 (tt) REVERT: A 547 PHE cc_start: 0.8812 (m-80) cc_final: 0.8018 (m-10) REVERT: A 643 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7536 (mm-30) REVERT: A 654 MET cc_start: 0.8460 (tpp) cc_final: 0.8069 (tpp) REVERT: A 684 ASN cc_start: 0.9162 (t0) cc_final: 0.8842 (t0) REVERT: B 4 ASN cc_start: 0.9456 (t0) cc_final: 0.8787 (t0) REVERT: B 7 LEU cc_start: 0.9636 (mt) cc_final: 0.9320 (mt) REVERT: B 52 THR cc_start: 0.8477 (t) cc_final: 0.8183 (t) REVERT: B 78 LEU cc_start: 0.8650 (tp) cc_final: 0.8367 (tp) REVERT: B 80 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9105 (mmtm) REVERT: B 87 ILE cc_start: 0.9412 (pt) cc_final: 0.9024 (mp) REVERT: B 112 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8330 (mp0) REVERT: B 133 ASP cc_start: 0.8389 (t70) cc_final: 0.7702 (m-30) REVERT: B 174 GLU cc_start: 0.8644 (tt0) cc_final: 0.7962 (tt0) REVERT: B 237 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8577 (mptt) REVERT: B 250 ILE cc_start: 0.8591 (mp) cc_final: 0.8369 (mp) REVERT: B 255 LYS cc_start: 0.8790 (tptt) cc_final: 0.8058 (tptt) REVERT: B 258 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6925 (mt-10) REVERT: B 312 ASN cc_start: 0.8990 (m110) cc_final: 0.8347 (m-40) REVERT: B 314 CYS cc_start: 0.8774 (m) cc_final: 0.8500 (m) REVERT: B 320 TYR cc_start: 0.8734 (m-10) cc_final: 0.8439 (m-10) REVERT: B 349 LYS cc_start: 0.9163 (pttm) cc_final: 0.8730 (ptpp) REVERT: B 375 MET cc_start: 0.8797 (mtp) cc_final: 0.8429 (mtp) REVERT: B 402 CYS cc_start: 0.8297 (t) cc_final: 0.7827 (t) REVERT: B 408 MET cc_start: 0.7597 (ttp) cc_final: 0.6932 (ttp) REVERT: B 423 MET cc_start: 0.9669 (mtp) cc_final: 0.9356 (mtp) REVERT: B 460 MET cc_start: 0.8421 (tpp) cc_final: 0.8215 (tpp) REVERT: B 490 LEU cc_start: 0.9119 (tp) cc_final: 0.8654 (tp) REVERT: B 496 MET cc_start: 0.8734 (mtm) cc_final: 0.8369 (mtt) REVERT: B 528 MET cc_start: 0.9091 (mtm) cc_final: 0.8848 (mtp) REVERT: B 547 MET cc_start: 0.9104 (tpp) cc_final: 0.8532 (ttm) REVERT: B 574 MET cc_start: 0.8343 (mmm) cc_final: 0.7945 (tpp) REVERT: B 587 LYS cc_start: 0.8321 (mmtm) cc_final: 0.8042 (mmmt) REVERT: B 599 MET cc_start: 0.8617 (tpp) cc_final: 0.8078 (tpt) REVERT: B 681 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 740 LYS cc_start: 0.8987 (mttt) cc_final: 0.8742 (mttt) REVERT: C 55 MET cc_start: 0.8348 (mmm) cc_final: 0.7800 (mmm) REVERT: C 102 ILE cc_start: 0.8977 (mt) cc_final: 0.8727 (mp) REVERT: C 103 THR cc_start: 0.9252 (p) cc_final: 0.8948 (t) REVERT: C 123 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8006 (mmmt) REVERT: C 127 MET cc_start: 0.8947 (mpp) cc_final: 0.8191 (mpp) REVERT: C 170 THR cc_start: 0.7862 (p) cc_final: 0.6810 (p) REVERT: C 171 MET cc_start: 0.8167 (mmt) cc_final: 0.7844 (mmt) REVERT: C 213 MET cc_start: 0.9024 (ptm) cc_final: 0.8319 (ppp) REVERT: C 218 PHE cc_start: 0.8274 (m-10) cc_final: 0.7140 (m-80) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1113 time to fit residues: 57.7277 Evaluate side-chains 288 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 0.0370 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105627 restraints weight = 27647.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108890 restraints weight = 16210.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111096 restraints weight = 10924.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112598 restraints weight = 8180.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113640 restraints weight = 6629.508| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12545 Z= 0.135 Angle : 0.632 10.400 16962 Z= 0.323 Chirality : 0.042 0.184 1855 Planarity : 0.004 0.049 2070 Dihedral : 11.309 74.077 1924 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1441 helix: 0.43 (0.20), residues: 658 sheet: -1.56 (0.54), residues: 105 loop : -2.48 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 625 TYR 0.029 0.002 TYR B 6 PHE 0.023 0.001 PHE A 292 TRP 0.015 0.001 TRP C 83 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12545) covalent geometry : angle 0.63193 / 0.32 (16962) hydrogen bonds : bond 0.04319 / 2.87 ( 531) hydrogen bonds : angle 4.70798 / 3.31 ( 1457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ILE cc_start: 0.9383 (mt) cc_final: 0.8850 (tt) REVERT: A 261 TYR cc_start: 0.7914 (t80) cc_final: 0.7531 (t80) REVERT: A 340 ASP cc_start: 0.8851 (t0) cc_final: 0.8449 (t70) REVERT: A 442 LYS cc_start: 0.8960 (mttm) cc_final: 0.8501 (mmtp) REVERT: A 453 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7379 (tp30) REVERT: A 517 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7932 (tppt) REVERT: A 547 PHE cc_start: 0.8797 (m-80) cc_final: 0.8482 (m-80) REVERT: A 601 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8712 (mmp80) REVERT: A 643 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7545 (mm-30) REVERT: A 654 MET cc_start: 0.8491 (tpp) cc_final: 0.8009 (tpp) REVERT: A 684 ASN cc_start: 0.9201 (t0) cc_final: 0.8901 (t0) REVERT: A 692 ASP cc_start: 0.8570 (t0) cc_final: 0.8012 (t0) REVERT: B 4 ASN cc_start: 0.9356 (t0) cc_final: 0.8645 (t0) REVERT: B 7 LEU cc_start: 0.9611 (mt) cc_final: 0.9385 (mt) REVERT: B 41 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 52 THR cc_start: 0.8515 (t) cc_final: 0.8221 (t) REVERT: B 78 LEU cc_start: 0.8656 (tp) cc_final: 0.8379 (tp) REVERT: B 80 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9103 (mmtm) REVERT: B 87 ILE cc_start: 0.9206 (pt) cc_final: 0.8985 (mp) REVERT: B 174 GLU cc_start: 0.8689 (tt0) cc_final: 0.8090 (tt0) REVERT: B 221 LYS cc_start: 0.9416 (mttt) cc_final: 0.9208 (tttt) REVERT: B 237 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8664 (mptt) REVERT: B 250 ILE cc_start: 0.8702 (mp) cc_final: 0.8439 (mp) REVERT: B 255 LYS cc_start: 0.8797 (tptt) cc_final: 0.8063 (tptt) REVERT: B 266 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7831 (mt-10) REVERT: B 312 ASN cc_start: 0.8933 (m110) cc_final: 0.8238 (m-40) REVERT: B 314 CYS cc_start: 0.8830 (m) cc_final: 0.8540 (m) REVERT: B 320 TYR cc_start: 0.8674 (m-10) cc_final: 0.8352 (m-10) REVERT: B 336 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8837 (mttp) REVERT: B 375 MET cc_start: 0.8790 (mtp) cc_final: 0.8474 (mtp) REVERT: B 383 ASN cc_start: 0.8535 (m110) cc_final: 0.8247 (m110) REVERT: B 402 CYS cc_start: 0.8345 (t) cc_final: 0.7936 (t) REVERT: B 408 MET cc_start: 0.7368 (ttp) cc_final: 0.6568 (ttp) REVERT: B 423 MET cc_start: 0.9659 (mtp) cc_final: 0.9389 (mtp) REVERT: B 462 MET cc_start: 0.8193 (mtm) cc_final: 0.7986 (mtp) REVERT: B 478 MET cc_start: 0.8355 (ttp) cc_final: 0.7497 (tmm) REVERT: B 490 LEU cc_start: 0.9071 (tp) cc_final: 0.8485 (tp) REVERT: B 496 MET cc_start: 0.8691 (mtm) cc_final: 0.8387 (mtt) REVERT: B 528 MET cc_start: 0.9095 (mtm) cc_final: 0.8850 (mtp) REVERT: B 547 MET cc_start: 0.9108 (tpp) cc_final: 0.8544 (ttm) REVERT: B 574 MET cc_start: 0.8454 (mmm) cc_final: 0.8046 (tpp) REVERT: B 587 LYS cc_start: 0.8349 (mmtm) cc_final: 0.8056 (mmmt) REVERT: B 599 MET cc_start: 0.8696 (tpp) cc_final: 0.8176 (tpt) REVERT: B 740 LYS cc_start: 0.9061 (mttt) cc_final: 0.8826 (mttt) REVERT: C 9 LYS cc_start: 0.8011 (mttt) cc_final: 0.7779 (mttp) REVERT: C 55 MET cc_start: 0.8404 (mmm) cc_final: 0.7897 (mmm) REVERT: C 81 ASP cc_start: 0.7419 (t0) cc_final: 0.6885 (t0) REVERT: C 102 ILE cc_start: 0.9073 (mt) cc_final: 0.8797 (mp) REVERT: C 103 THR cc_start: 0.9248 (p) cc_final: 0.8917 (t) REVERT: C 123 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8156 (mmmt) REVERT: C 170 THR cc_start: 0.7879 (p) cc_final: 0.6989 (p) REVERT: C 171 MET cc_start: 0.7971 (mmt) cc_final: 0.7723 (mmt) REVERT: C 213 MET cc_start: 0.9082 (ptm) cc_final: 0.8362 (ppp) REVERT: C 218 PHE cc_start: 0.8310 (m-10) cc_final: 0.7221 (m-80) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1147 time to fit residues: 60.9342 Evaluate side-chains 292 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 116 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN B 348 ASN B 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107192 restraints weight = 27494.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110479 restraints weight = 16062.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112671 restraints weight = 10810.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114108 restraints weight = 8097.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115269 restraints weight = 6587.055| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12545 Z= 0.131 Angle : 0.652 10.526 16962 Z= 0.331 Chirality : 0.042 0.187 1855 Planarity : 0.004 0.053 2070 Dihedral : 11.284 73.922 1924 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1441 helix: 0.34 (0.20), residues: 663 sheet: -1.71 (0.53), residues: 102 loop : -2.40 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 45 TYR 0.023 0.001 TYR B 6 PHE 0.021 0.001 PHE C 126 TRP 0.027 0.001 TRP A 381 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12545) covalent geometry : angle 0.65162 / 0.33 (16962) hydrogen bonds : bond 0.04299 / 2.85 ( 531) hydrogen bonds : angle 4.59604 / 3.24 ( 1457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7801 (t80) cc_final: 0.7518 (t80) REVERT: A 340 ASP cc_start: 0.8807 (t0) cc_final: 0.8374 (t70) REVERT: A 406 MET cc_start: 0.7182 (ttt) cc_final: 0.6809 (ttp) REVERT: A 409 MET cc_start: 0.8603 (mmm) cc_final: 0.8265 (mmm) REVERT: A 453 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7350 (tp30) REVERT: A 517 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8008 (tppt) REVERT: A 547 PHE cc_start: 0.8774 (m-80) cc_final: 0.8355 (m-80) REVERT: A 596 MET cc_start: 0.8598 (tpp) cc_final: 0.8350 (tpt) REVERT: A 639 ASP cc_start: 0.7822 (t0) cc_final: 0.7596 (t0) REVERT: A 654 MET cc_start: 0.8480 (tpp) cc_final: 0.8021 (tpp) REVERT: A 684 ASN cc_start: 0.9163 (t0) cc_final: 0.8796 (t0) REVERT: A 692 ASP cc_start: 0.8536 (t0) cc_final: 0.8151 (t0) REVERT: B 45 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7770 (mtp85) REVERT: B 52 THR cc_start: 0.8447 (t) cc_final: 0.8165 (t) REVERT: B 80 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9082 (mmtm) REVERT: B 147 GLN cc_start: 0.8564 (tp40) cc_final: 0.8260 (tm-30) REVERT: B 174 GLU cc_start: 0.8684 (tt0) cc_final: 0.8029 (tt0) REVERT: B 221 LYS cc_start: 0.9426 (mttt) cc_final: 0.9173 (tttt) REVERT: B 237 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8582 (mptt) REVERT: B 250 ILE cc_start: 0.8672 (mp) cc_final: 0.8437 (mp) REVERT: B 255 LYS cc_start: 0.8608 (tptt) cc_final: 0.8222 (tptt) REVERT: B 312 ASN cc_start: 0.8936 (m110) cc_final: 0.8162 (m-40) REVERT: B 320 TYR cc_start: 0.8625 (m-10) cc_final: 0.8378 (m-10) REVERT: B 336 LYS cc_start: 0.9275 (ttpp) cc_final: 0.8890 (mttp) REVERT: B 375 MET cc_start: 0.8786 (mtp) cc_final: 0.8430 (mtp) REVERT: B 402 CYS cc_start: 0.8190 (t) cc_final: 0.7960 (t) REVERT: B 408 MET cc_start: 0.7340 (ttp) cc_final: 0.6527 (ttp) REVERT: B 423 MET cc_start: 0.9616 (mtp) cc_final: 0.9326 (mtp) REVERT: B 442 LEU cc_start: 0.8671 (tp) cc_final: 0.8104 (tp) REVERT: B 462 MET cc_start: 0.8192 (mtm) cc_final: 0.7953 (mtp) REVERT: B 490 LEU cc_start: 0.9053 (tp) cc_final: 0.8498 (tp) REVERT: B 496 MET cc_start: 0.8723 (mtm) cc_final: 0.8075 (mtt) REVERT: B 520 GLU cc_start: 0.8561 (pm20) cc_final: 0.8129 (pm20) REVERT: B 528 MET cc_start: 0.9079 (mtm) cc_final: 0.8843 (mtp) REVERT: B 547 MET cc_start: 0.9054 (tpp) cc_final: 0.8549 (ttm) REVERT: B 574 MET cc_start: 0.8184 (mmm) cc_final: 0.7859 (tpp) REVERT: B 587 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8053 (mmmt) REVERT: B 599 MET cc_start: 0.8746 (tpp) cc_final: 0.8288 (tpt) REVERT: C 9 LYS cc_start: 0.7990 (mttt) cc_final: 0.7760 (mttp) REVERT: C 55 MET cc_start: 0.8460 (mmm) cc_final: 0.7946 (mmm) REVERT: C 81 ASP cc_start: 0.7443 (t0) cc_final: 0.7115 (t0) REVERT: C 102 ILE cc_start: 0.9059 (mt) cc_final: 0.8799 (mp) REVERT: C 103 THR cc_start: 0.9277 (p) cc_final: 0.8874 (t) REVERT: C 123 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8085 (mmmt) REVERT: C 127 MET cc_start: 0.8904 (mpp) cc_final: 0.8233 (mpp) REVERT: C 213 MET cc_start: 0.9057 (ptm) cc_final: 0.8362 (ppp) REVERT: C 218 PHE cc_start: 0.8313 (m-10) cc_final: 0.7221 (m-80) REVERT: C 224 PHE cc_start: 0.8808 (t80) cc_final: 0.8523 (t80) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1149 time to fit residues: 58.9250 Evaluate side-chains 295 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 HIS A 640 ASN B 348 ASN B 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.128819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104941 restraints weight = 27866.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108103 restraints weight = 16473.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110269 restraints weight = 11222.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111629 restraints weight = 8456.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112770 restraints weight = 6932.326| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12545 Z= 0.164 Angle : 0.672 10.239 16962 Z= 0.345 Chirality : 0.044 0.180 1855 Planarity : 0.005 0.060 2070 Dihedral : 11.288 73.970 1924 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.15 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.22), residues: 1441 helix: 0.34 (0.20), residues: 661 sheet: -1.85 (0.53), residues: 99 loop : -2.41 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 235 TYR 0.024 0.002 TYR B 6 PHE 0.023 0.002 PHE C 212 TRP 0.032 0.002 TRP A 381 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12545) covalent geometry : angle 0.67214 / 0.35 (16962) hydrogen bonds : bond 0.04519 / 2.99 ( 531) hydrogen bonds : angle 4.73422 / 3.36 ( 1457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8992 (t80) cc_final: 0.8705 (t80) REVERT: A 261 TYR cc_start: 0.7858 (t80) cc_final: 0.7654 (t80) REVERT: A 340 ASP cc_start: 0.8741 (t0) cc_final: 0.8464 (t70) REVERT: A 406 MET cc_start: 0.6967 (ttt) cc_final: 0.6665 (ttp) REVERT: A 409 MET cc_start: 0.8590 (mmm) cc_final: 0.8336 (mmm) REVERT: A 442 LYS cc_start: 0.9024 (mttm) cc_final: 0.8667 (mmtp) REVERT: A 453 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7279 (tp30) REVERT: A 547 PHE cc_start: 0.8830 (m-80) cc_final: 0.8355 (m-80) REVERT: A 596 MET cc_start: 0.8444 (tpp) cc_final: 0.8237 (tpt) REVERT: A 619 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8359 (mmpt) REVERT: A 639 ASP cc_start: 0.8080 (t0) cc_final: 0.7500 (t0) REVERT: A 654 MET cc_start: 0.8480 (tpp) cc_final: 0.8192 (tpp) REVERT: A 684 ASN cc_start: 0.9232 (t0) cc_final: 0.8984 (t0) REVERT: A 692 ASP cc_start: 0.8591 (t0) cc_final: 0.8172 (t0) REVERT: B 45 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7617 (mtp85) REVERT: B 52 THR cc_start: 0.8571 (t) cc_final: 0.8316 (t) REVERT: B 80 LYS cc_start: 0.9318 (mmmm) cc_final: 0.9057 (mmtm) REVERT: B 85 VAL cc_start: 0.9133 (t) cc_final: 0.8918 (t) REVERT: B 90 MET cc_start: 0.8913 (ptm) cc_final: 0.8689 (ptm) REVERT: B 147 GLN cc_start: 0.8628 (tp40) cc_final: 0.8169 (tm-30) REVERT: B 174 GLU cc_start: 0.8748 (tt0) cc_final: 0.8047 (tt0) REVERT: B 221 LYS cc_start: 0.9450 (mttt) cc_final: 0.9217 (tttt) REVERT: B 237 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8657 (mptt) REVERT: B 250 ILE cc_start: 0.8782 (mp) cc_final: 0.8569 (mp) REVERT: B 255 LYS cc_start: 0.8796 (tptt) cc_final: 0.8232 (tptt) REVERT: B 258 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6868 (mt-10) REVERT: B 312 ASN cc_start: 0.8960 (m110) cc_final: 0.8320 (m-40) REVERT: B 320 TYR cc_start: 0.8663 (m-10) cc_final: 0.8413 (m-10) REVERT: B 336 LYS cc_start: 0.9270 (ttpp) cc_final: 0.8894 (mttp) REVERT: B 375 MET cc_start: 0.8791 (mtp) cc_final: 0.8512 (mtp) REVERT: B 402 CYS cc_start: 0.8212 (t) cc_final: 0.7912 (t) REVERT: B 408 MET cc_start: 0.7643 (ttp) cc_final: 0.6901 (ttp) REVERT: B 409 LEU cc_start: 0.7872 (mt) cc_final: 0.7501 (mp) REVERT: B 423 MET cc_start: 0.9618 (mtp) cc_final: 0.9390 (mtp) REVERT: B 462 MET cc_start: 0.8201 (mtm) cc_final: 0.7919 (mtp) REVERT: B 496 MET cc_start: 0.8718 (mtm) cc_final: 0.8395 (mtt) REVERT: B 547 MET cc_start: 0.9018 (tpp) cc_final: 0.8452 (mmm) REVERT: B 574 MET cc_start: 0.8236 (mmm) cc_final: 0.7869 (tpp) REVERT: B 587 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7933 (mmmt) REVERT: B 736 TYR cc_start: 0.8467 (t80) cc_final: 0.7990 (t80) REVERT: C 10 GLU cc_start: 0.9294 (mp0) cc_final: 0.8809 (mp0) REVERT: C 55 MET cc_start: 0.8505 (mmm) cc_final: 0.8018 (mmm) REVERT: C 81 ASP cc_start: 0.7588 (t0) cc_final: 0.7268 (t0) REVERT: C 102 ILE cc_start: 0.9125 (mt) cc_final: 0.8856 (mp) REVERT: C 103 THR cc_start: 0.9252 (p) cc_final: 0.8915 (t) REVERT: C 123 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8126 (mmmt) REVERT: C 127 MET cc_start: 0.8872 (mpp) cc_final: 0.8087 (mpp) REVERT: C 213 MET cc_start: 0.9120 (ptm) cc_final: 0.8424 (ppp) REVERT: C 218 PHE cc_start: 0.8375 (m-10) cc_final: 0.7341 (m-80) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1177 time to fit residues: 59.0394 Evaluate side-chains 291 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 70 optimal weight: 0.0980 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 383 ASN C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106416 restraints weight = 27794.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109677 restraints weight = 16385.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111894 restraints weight = 11111.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113261 restraints weight = 8331.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114429 restraints weight = 6836.499| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12545 Z= 0.131 Angle : 0.671 11.048 16962 Z= 0.342 Chirality : 0.043 0.185 1855 Planarity : 0.004 0.055 2070 Dihedral : 11.257 73.801 1924 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1441 helix: 0.33 (0.20), residues: 661 sheet: -1.79 (0.53), residues: 103 loop : -2.35 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 131 TYR 0.061 0.002 TYR B 736 PHE 0.018 0.001 PHE B 183 TRP 0.024 0.001 TRP A 381 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12545) covalent geometry : angle 0.67067 / 0.34 (16962) hydrogen bonds : bond 0.04394 / 2.90 ( 531) hydrogen bonds : angle 4.63398 / 3.29 ( 1457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8940 (t80) cc_final: 0.8693 (t80) REVERT: A 261 TYR cc_start: 0.7795 (t80) cc_final: 0.7558 (t80) REVERT: A 275 LYS cc_start: 0.8903 (pttp) cc_final: 0.8080 (pptt) REVERT: A 287 ILE cc_start: 0.9285 (tp) cc_final: 0.8987 (tp) REVERT: A 340 ASP cc_start: 0.8734 (t0) cc_final: 0.8409 (t70) REVERT: A 409 MET cc_start: 0.8549 (mmm) cc_final: 0.8317 (mmm) REVERT: A 453 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 547 PHE cc_start: 0.8934 (m-80) cc_final: 0.8347 (m-80) REVERT: A 639 ASP cc_start: 0.8054 (t0) cc_final: 0.6905 (m-30) REVERT: A 650 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8591 (pttm) REVERT: A 654 MET cc_start: 0.8445 (tpp) cc_final: 0.8136 (tpp) REVERT: A 684 ASN cc_start: 0.9180 (t0) cc_final: 0.8746 (t0) REVERT: A 692 ASP cc_start: 0.8565 (t0) cc_final: 0.8127 (t0) REVERT: B 45 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7852 (mtp85) REVERT: B 52 THR cc_start: 0.8506 (t) cc_final: 0.8233 (t) REVERT: B 80 LYS cc_start: 0.9289 (mmmm) cc_final: 0.9069 (mmtm) REVERT: B 85 VAL cc_start: 0.9167 (t) cc_final: 0.8943 (t) REVERT: B 87 ILE cc_start: 0.9244 (pt) cc_final: 0.8769 (pt) REVERT: B 109 CYS cc_start: 0.8693 (m) cc_final: 0.7167 (p) REVERT: B 140 MET cc_start: 0.7466 (tpp) cc_final: 0.6768 (ttm) REVERT: B 147 GLN cc_start: 0.8634 (tp40) cc_final: 0.8123 (tm-30) REVERT: B 174 GLU cc_start: 0.8712 (tt0) cc_final: 0.8038 (tt0) REVERT: B 221 LYS cc_start: 0.9441 (mttt) cc_final: 0.9198 (tttt) REVERT: B 237 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8641 (mptt) REVERT: B 250 ILE cc_start: 0.8829 (mp) cc_final: 0.8616 (mp) REVERT: B 255 LYS cc_start: 0.8782 (tptt) cc_final: 0.8188 (tptt) REVERT: B 258 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6891 (mt-10) REVERT: B 312 ASN cc_start: 0.8979 (m110) cc_final: 0.8221 (m-40) REVERT: B 336 LYS cc_start: 0.9286 (ttpp) cc_final: 0.8846 (mttp) REVERT: B 375 MET cc_start: 0.8779 (mtp) cc_final: 0.8447 (mtp) REVERT: B 402 CYS cc_start: 0.8197 (t) cc_final: 0.7942 (t) REVERT: B 408 MET cc_start: 0.7539 (ttp) cc_final: 0.6792 (ttp) REVERT: B 423 MET cc_start: 0.9590 (mtp) cc_final: 0.9376 (mtp) REVERT: B 442 LEU cc_start: 0.8775 (tp) cc_final: 0.8283 (tp) REVERT: B 462 MET cc_start: 0.8121 (mtm) cc_final: 0.7886 (mtp) REVERT: B 496 MET cc_start: 0.8741 (mtm) cc_final: 0.8091 (mtt) REVERT: B 520 GLU cc_start: 0.8538 (pm20) cc_final: 0.8138 (pm20) REVERT: B 528 MET cc_start: 0.8979 (mtp) cc_final: 0.8738 (mtt) REVERT: B 547 MET cc_start: 0.9014 (tpp) cc_final: 0.8475 (ttm) REVERT: B 574 MET cc_start: 0.8217 (mmm) cc_final: 0.7814 (tpp) REVERT: B 587 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7923 (mmmt) REVERT: B 617 MET cc_start: 0.7679 (mtm) cc_final: 0.7074 (mtm) REVERT: C 10 GLU cc_start: 0.9196 (mp0) cc_final: 0.8566 (mp0) REVERT: C 55 MET cc_start: 0.8460 (mmm) cc_final: 0.8104 (mmm) REVERT: C 81 ASP cc_start: 0.7171 (t0) cc_final: 0.6781 (t0) REVERT: C 85 LYS cc_start: 0.5809 (mmtm) cc_final: 0.5551 (mmmt) REVERT: C 102 ILE cc_start: 0.9124 (mt) cc_final: 0.8851 (mp) REVERT: C 103 THR cc_start: 0.9206 (p) cc_final: 0.8859 (t) REVERT: C 123 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8137 (mmmt) REVERT: C 127 MET cc_start: 0.8814 (mpp) cc_final: 0.8107 (mpp) REVERT: C 213 MET cc_start: 0.9096 (ptm) cc_final: 0.8394 (ppp) REVERT: C 218 PHE cc_start: 0.8380 (m-10) cc_final: 0.7383 (m-80) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1164 time to fit residues: 59.5042 Evaluate side-chains 309 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106290 restraints weight = 27665.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109514 restraints weight = 16258.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111753 restraints weight = 11001.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113262 restraints weight = 8241.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114310 restraints weight = 6699.818| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12545 Z= 0.130 Angle : 0.653 9.970 16962 Z= 0.333 Chirality : 0.043 0.184 1855 Planarity : 0.004 0.053 2070 Dihedral : 11.229 73.757 1924 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.22), residues: 1441 helix: 0.44 (0.20), residues: 656 sheet: -1.79 (0.53), residues: 100 loop : -2.27 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 131 TYR 0.047 0.002 TYR B 6 PHE 0.017 0.001 PHE B 108 TRP 0.021 0.001 TRP A 381 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12545) covalent geometry : angle 0.65333 / 0.33 (16962) hydrogen bonds : bond 0.04362 / 2.91 ( 531) hydrogen bonds : angle 4.56881 / 3.25 ( 1457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.58 seconds wall clock time: 37 minutes 56.26 seconds (2276.26 seconds total)