Starting phenix.real_space_refine on Sat Sep 12 05:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kuv_9888/09_2026/6kuv_9888_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kuv_9888/09_2026/6kuv_9888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kuv_9888/09_2026/6kuv_9888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kuv_9888/09_2026/6kuv_9888.map" model { file = "/net/cci-nas-00/data/ceres_data/6kuv_9888/09_2026/6kuv_9888_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kuv_9888/09_2026/6kuv_9888_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 116 5.16 5 C 8629 2.51 5 N 2338 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 13720 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5625 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 661} Chain breaks: 3 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: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5599 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 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: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 3} Chain: "V" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 285 Classifications: {'RNA': 13} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 8} Time building chain proxies: 2.85, per 1000 atoms: 0.21 Number of scatterers: 13720 At special positions: 0 Unit cell: (110.16, 127.84, 122.4, 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 116 16.00 P 23 15.00 O 2614 8.00 N 2338 7.00 C 8629 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: 0.97 Conformation dependent library (CDL) restraints added in 612.8 milliseconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 48.5% alpha, 7.7% beta 4 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.989A pdb=" N ASN A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 removed outlier: 4.047A pdb=" N ILE A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 150 through 170 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.515A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.186A 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 296 through 300 removed outlier: 3.712A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) 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 removed outlier: 3.545A pdb=" N GLU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.703A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 568 removed outlier: 3.584A pdb=" N ARG A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 569 through 589 removed outlier: 4.335A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 637 removed outlier: 3.822A pdb=" N MET A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.601A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.619A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 12 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.782A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.797A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.589A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.543A 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: 3.590A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.811A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.752A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.762A 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 392 removed outlier: 3.642A pdb=" N THR B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.726A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.539A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.775A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 668 through 672 removed outlier: 4.170A pdb=" N LEU B 671 " --> pdb=" O ARG B 668 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 672 " --> pdb=" O THR B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 672' Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.858A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.657A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.642A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.790A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.690A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.722A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.696A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.720A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.220A pdb=" N GLU C 178 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 179' Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.741A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.543A pdb=" N ARG C 235 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU C 237 " --> pdb=" O GLU C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.561A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 243' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.341A pdb=" N GLU A 105 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE A 133 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY A 107 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.555A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.358A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.538A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.502A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.601A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 567 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3745 1.33 - 1.46: 2605 1.46 - 1.58: 7448 1.58 - 1.70: 44 1.70 - 1.82: 192 Bond restraints: 14034 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.378 -0.045 8.40e-03 1.42e+04 2.84e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.27e-02 6.20e+03 1.76e+01 bond pdb=" C LEU B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.12e+00 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.25e-02 6.40e+03 5.00e+00 ... (remaining 14029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18396 2.04 - 4.09: 482 4.09 - 6.13: 60 6.13 - 8.18: 25 8.18 - 10.22: 3 Bond angle restraints: 18966 Sorted by residual: angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.53 106.94 6.59 9.80e-01 1.04e+00 4.52e+01 angle pdb=" N ILE B 393 " pdb=" CA ILE B 393 " pdb=" C ILE B 393 " ideal model delta sigma weight residual 113.20 107.64 5.56 9.60e-01 1.09e+00 3.35e+01 angle pdb=" C1' C R 7 " pdb=" N1 C R 7 " pdb=" C2 C R 7 " ideal model delta sigma weight residual 118.80 124.05 -5.25 1.10e+00 8.26e-01 2.27e+01 angle pdb=" C1' U V 5 " pdb=" N1 U V 5 " pdb=" C2 U V 5 " ideal model delta sigma weight residual 117.70 122.98 -5.28 1.20e+00 6.94e-01 1.93e+01 angle pdb=" N1 C R 7 " pdb=" C2 C R 7 " pdb=" O2 C R 7 " ideal model delta sigma weight residual 118.90 121.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 18961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8531 35.86 - 71.72: 82 71.72 - 107.57: 8 107.57 - 143.43: 0 143.43 - 179.29: 4 Dihedral angle restraints: 8625 sinusoidal: 3837 harmonic: 4788 Sorted by residual: dihedral pdb=" O4' U V 5 " pdb=" C1' U V 5 " pdb=" N1 U V 5 " pdb=" C2 U V 5 " ideal model delta sinusoidal sigma weight residual 232.00 52.71 179.29 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 7 " pdb=" C1' C R 7 " pdb=" N1 C R 7 " pdb=" C2 C R 7 " ideal model delta sinusoidal sigma weight residual -128.00 51.08 -179.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 4 " pdb=" C1' U R 4 " pdb=" N1 U R 4 " pdb=" C2 U R 4 " ideal model delta sinusoidal sigma weight residual -128.00 48.06 -176.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1645 0.058 - 0.116: 359 0.116 - 0.174: 66 0.174 - 0.232: 5 0.232 - 0.290: 4 Chirality restraints: 2079 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 2.36 0.29 2.00e-01 2.50e+01 2.10e+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 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2076 not shown) Planarity restraints: 2333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 422 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.21e+01 pdb=" C LYS A 422 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS A 422 " 0.023 2.00e-02 2.50e+03 pdb=" N MET A 423 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 423 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C MET A 423 " 0.060 2.00e-02 2.50e+03 pdb=" O MET A 423 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS A 424 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 628 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE A 628 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 628 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 629 " -0.020 2.00e-02 2.50e+03 ... (remaining 2330 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1198 2.75 - 3.28: 12752 3.28 - 3.82: 20932 3.82 - 4.36: 25381 4.36 - 4.90: 43484 Nonbonded interactions: 103747 Sorted by model distance: nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.206 3.120 nonbonded pdb=" OE2 GLU A 408 " pdb=" NH2 ARG B 557 " model vdw 2.230 3.120 nonbonded pdb=" OH TYR B 320 " pdb=" OG SER B 417 " model vdw 2.287 3.040 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.289 3.040 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.293 3.040 ... (remaining 103742 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: 0.000 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14034 Z= 0.197 Angle : 0.802 10.221 18966 Z= 0.485 Chirality : 0.051 0.290 2079 Planarity : 0.006 0.065 2333 Dihedral : 11.910 179.287 5517 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 0.28 % Allowed : 2.28 % Favored : 97.44 % 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: -4.84 (0.15), residues: 1618 helix: -3.33 (0.12), residues: 716 sheet: -1.95 (0.45), residues: 138 loop : -3.31 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 438 TYR 0.017 0.002 TYR B 38 PHE 0.022 0.002 PHE B 420 TRP 0.032 0.003 TRP A 386 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.20 (14034) covalent geometry : angle 0.80216 / 0.48 (18966) hydrogen bonds : bond 0.14342 / 9.45 ( 578) hydrogen bonds : angle 9.53900 / 6.63 ( 1627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 598 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4421 (ttp80) cc_final: 0.3886 (mtm-85) REVERT: A 43 GLN cc_start: 0.7455 (tt0) cc_final: 0.7218 (tp-100) REVERT: A 121 PHE cc_start: 0.4748 (t80) cc_final: 0.4487 (t80) REVERT: A 291 PHE cc_start: 0.7881 (m-80) cc_final: 0.6788 (m-80) REVERT: A 419 TYR cc_start: 0.7819 (t80) cc_final: 0.7532 (t80) REVERT: A 435 ASN cc_start: 0.7487 (m-40) cc_final: 0.6975 (t0) REVERT: A 457 PHE cc_start: 0.8099 (m-80) cc_final: 0.7548 (m-80) REVERT: A 492 ASN cc_start: 0.6371 (m-40) cc_final: 0.5659 (p0) REVERT: A 578 GLU cc_start: 0.7817 (tt0) cc_final: 0.7124 (tt0) REVERT: A 653 LEU cc_start: 0.8042 (mp) cc_final: 0.7715 (mp) REVERT: B 46 THR cc_start: 0.8474 (m) cc_final: 0.7941 (t) REVERT: B 90 MET cc_start: 0.8749 (ppp) cc_final: 0.8515 (ptm) REVERT: B 138 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6742 (ttm-80) REVERT: B 180 GLU cc_start: 0.6231 (tt0) cc_final: 0.5987 (mp0) REVERT: B 219 PHE cc_start: 0.8465 (t80) cc_final: 0.8026 (t80) REVERT: B 357 PHE cc_start: 0.6732 (p90) cc_final: 0.6362 (p90) REVERT: B 446 ASP cc_start: 0.8334 (p0) cc_final: 0.7588 (p0) REVERT: B 494 THR cc_start: 0.8449 (p) cc_final: 0.8129 (p) REVERT: B 547 MET cc_start: 0.7978 (tpp) cc_final: 0.7711 (tpp) REVERT: B 574 MET cc_start: 0.7858 (mmm) cc_final: 0.7165 (mmm) REVERT: B 610 GLU cc_start: 0.7169 (mp0) cc_final: 0.6591 (mp0) REVERT: C 11 TYR cc_start: 0.7078 (t80) cc_final: 0.6652 (t80) REVERT: C 55 MET cc_start: 0.8904 (mmm) cc_final: 0.8359 (tpp) REVERT: C 156 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8107 (Cg_endo) REVERT: C 178 GLU cc_start: 0.5513 (pp20) cc_final: 0.5105 (pp20) REVERT: C 209 VAL cc_start: 0.9236 (t) cc_final: 0.9036 (t) REVERT: C 225 LEU cc_start: 0.8192 (mt) cc_final: 0.7971 (mt) outliers start: 4 outliers final: 0 residues processed: 602 average time/residue: 0.1323 time to fit residues: 110.7280 Evaluate side-chains 322 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0070 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS A 210 HIS A 311 GLN A 515 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 647 ASN A 670 GLN B 11 ASN B 70 ASN B 84 ASN B 147 GLN B 383 ASN B 436 ASN B 477 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138866 restraints weight = 22904.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141670 restraints weight = 14818.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143609 restraints weight = 10814.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144779 restraints weight = 8681.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145811 restraints weight = 7485.938| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14034 Z= 0.152 Angle : 0.666 8.833 18966 Z= 0.346 Chirality : 0.044 0.190 2079 Planarity : 0.005 0.047 2333 Dihedral : 13.268 179.902 2115 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 0.21 % Allowed : 3.45 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.18), residues: 1618 helix: -1.57 (0.16), residues: 748 sheet: -1.27 (0.50), residues: 128 loop : -3.14 (0.18), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 133 TYR 0.016 0.001 TYR A 549 PHE 0.023 0.002 PHE A 341 TRP 0.021 0.002 TRP A 388 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (14034) covalent geometry : angle 0.66597 / 0.35 (18966) hydrogen bonds : bond 0.05492 / 3.58 ( 578) hydrogen bonds : angle 6.13591 / 4.25 ( 1627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 406 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4554 (ttp80) cc_final: 0.3707 (mtm-85) REVERT: A 120 LYS cc_start: 0.6750 (mmtm) cc_final: 0.6458 (mttp) REVERT: A 291 PHE cc_start: 0.7947 (m-80) cc_final: 0.6435 (m-80) REVERT: A 368 GLU cc_start: 0.5134 (pt0) cc_final: 0.4899 (pt0) REVERT: A 419 TYR cc_start: 0.7830 (t80) cc_final: 0.7470 (t80) REVERT: A 423 MET cc_start: 0.8381 (mmm) cc_final: 0.7935 (mmt) REVERT: A 492 ASN cc_start: 0.6240 (m-40) cc_final: 0.5498 (p0) REVERT: A 497 MET cc_start: 0.6590 (mtt) cc_final: 0.6173 (mtt) REVERT: A 504 GLU cc_start: 0.8238 (mp0) cc_final: 0.8022 (mp0) REVERT: A 578 GLU cc_start: 0.7804 (tt0) cc_final: 0.6958 (tt0) REVERT: A 590 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 591 ASN cc_start: 0.7039 (t0) cc_final: 0.6323 (t0) REVERT: A 653 LEU cc_start: 0.8204 (mp) cc_final: 0.7685 (mp) REVERT: B 17 MET cc_start: 0.6422 (mpp) cc_final: 0.5883 (mpp) REVERT: B 138 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.6939 (ttm-80) REVERT: B 357 PHE cc_start: 0.6548 (p90) cc_final: 0.6287 (p90) REVERT: B 375 MET cc_start: 0.7689 (mtm) cc_final: 0.7377 (mtp) REVERT: B 382 MET cc_start: 0.7105 (mtp) cc_final: 0.6727 (mmt) REVERT: B 388 ASP cc_start: 0.8463 (m-30) cc_final: 0.7949 (m-30) REVERT: B 610 GLU cc_start: 0.6954 (mp0) cc_final: 0.6696 (mp0) REVERT: C 156 PRO cc_start: 0.8126 (Cg_exo) cc_final: 0.7804 (Cg_endo) REVERT: C 225 LEU cc_start: 0.8491 (mt) cc_final: 0.8202 (mt) outliers start: 3 outliers final: 1 residues processed: 408 average time/residue: 0.1111 time to fit residues: 66.5830 Evaluate side-chains 298 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 18 optimal weight: 0.8980 chunk 122 optimal weight: 0.0970 chunk 39 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 670 GLN B 11 ASN B 70 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138432 restraints weight = 22883.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141164 restraints weight = 14867.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143026 restraints weight = 10868.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144315 restraints weight = 8691.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145184 restraints weight = 7421.242| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14034 Z= 0.145 Angle : 0.635 7.298 18966 Z= 0.328 Chirality : 0.042 0.184 2079 Planarity : 0.004 0.046 2333 Dihedral : 13.146 178.662 2115 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % 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: -2.48 (0.19), residues: 1618 helix: -0.56 (0.18), residues: 748 sheet: -1.10 (0.47), residues: 151 loop : -3.01 (0.19), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 693 TYR 0.020 0.001 TYR B 427 PHE 0.023 0.001 PHE B 420 TRP 0.018 0.001 TRP A 386 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14034) covalent geometry : angle 0.63501 / 0.33 (18966) hydrogen bonds : bond 0.04960 / 3.20 ( 578) hydrogen bonds : angle 5.41585 / 3.75 ( 1627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4420 (ttp80) cc_final: 0.3497 (mpp-170) REVERT: A 138 LYS cc_start: 0.6018 (mttt) cc_final: 0.5699 (mtmm) REVERT: A 171 MET cc_start: 0.5973 (pmm) cc_final: 0.5129 (pmm) REVERT: A 291 PHE cc_start: 0.7907 (m-80) cc_final: 0.7241 (m-80) REVERT: A 419 TYR cc_start: 0.7428 (t80) cc_final: 0.7015 (t80) REVERT: A 492 ASN cc_start: 0.6216 (m-40) cc_final: 0.5721 (p0) REVERT: A 555 MET cc_start: 0.8456 (mmm) cc_final: 0.7864 (mmm) REVERT: B 17 MET cc_start: 0.6277 (mpp) cc_final: 0.5669 (mpp) REVERT: B 77 ASN cc_start: 0.8147 (p0) cc_final: 0.7668 (p0) REVERT: B 138 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.7021 (ttm-80) REVERT: B 178 TRP cc_start: 0.6631 (m-10) cc_final: 0.6388 (m-10) REVERT: B 180 GLU cc_start: 0.6340 (tt0) cc_final: 0.5752 (tm-30) REVERT: B 357 PHE cc_start: 0.6507 (p90) cc_final: 0.6206 (p90) REVERT: B 375 MET cc_start: 0.7574 (mtm) cc_final: 0.7197 (mtp) REVERT: B 376 LYS cc_start: 0.8157 (tttt) cc_final: 0.7951 (tptt) REVERT: B 381 LEU cc_start: 0.7649 (mp) cc_final: 0.7363 (mt) REVERT: B 382 MET cc_start: 0.7203 (mtp) cc_final: 0.6873 (mmt) REVERT: B 391 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6744 (pt0) REVERT: B 610 GLU cc_start: 0.7068 (mp0) cc_final: 0.6736 (mp0) REVERT: C 5 LEU cc_start: 0.6838 (pt) cc_final: 0.6491 (pt) REVERT: C 9 LYS cc_start: 0.8181 (mttt) cc_final: 0.7742 (ptpt) REVERT: C 156 PRO cc_start: 0.8022 (Cg_exo) cc_final: 0.7819 (Cg_endo) REVERT: C 162 ASN cc_start: 0.6580 (p0) cc_final: 0.6186 (p0) REVERT: C 225 LEU cc_start: 0.8526 (mt) cc_final: 0.8248 (mt) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.1082 time to fit residues: 60.7629 Evaluate side-chains 279 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 124 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 11 ASN B 70 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135539 restraints weight = 23005.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138178 restraints weight = 15003.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140075 restraints weight = 11112.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141027 restraints weight = 8914.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141030 restraints weight = 7732.517| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14034 Z= 0.140 Angle : 0.611 7.484 18966 Z= 0.318 Chirality : 0.042 0.188 2079 Planarity : 0.004 0.045 2333 Dihedral : 13.088 178.385 2115 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.86 % Favored : 93.08 % Rotamer: Outliers : 0.14 % Allowed : 2.83 % Favored : 97.03 % 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: -2.07 (0.20), residues: 1618 helix: -0.09 (0.18), residues: 746 sheet: -0.94 (0.48), residues: 147 loop : -2.93 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.019 0.002 TYR A 419 PHE 0.020 0.001 PHE B 89 TRP 0.016 0.001 TRP A 386 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (14034) covalent geometry : angle 0.61144 / 0.32 (18966) hydrogen bonds : bond 0.04599 / 2.97 ( 578) hydrogen bonds : angle 5.11223 / 3.55 ( 1627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4341 (ttp80) cc_final: 0.3413 (mpp-170) REVERT: A 26 ARG cc_start: 0.5370 (mtt180) cc_final: 0.5123 (mtt180) REVERT: A 43 GLN cc_start: 0.7766 (tp40) cc_final: 0.7388 (tm-30) REVERT: A 120 LYS cc_start: 0.6566 (mmtm) cc_final: 0.6309 (mttp) REVERT: A 291 PHE cc_start: 0.8006 (m-80) cc_final: 0.7315 (m-80) REVERT: A 419 TYR cc_start: 0.7471 (t80) cc_final: 0.7232 (t80) REVERT: A 423 MET cc_start: 0.8051 (mtt) cc_final: 0.7653 (mtt) REVERT: A 492 ASN cc_start: 0.6401 (m-40) cc_final: 0.5863 (p0) REVERT: A 555 MET cc_start: 0.8401 (mmm) cc_final: 0.7718 (mmm) REVERT: A 578 GLU cc_start: 0.7807 (tt0) cc_final: 0.7106 (mt-10) REVERT: B 77 ASN cc_start: 0.8296 (p0) cc_final: 0.7978 (p0) REVERT: B 138 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.6909 (ttm-80) REVERT: B 178 TRP cc_start: 0.6597 (m-10) cc_final: 0.6335 (m-10) REVERT: B 180 GLU cc_start: 0.6401 (tt0) cc_final: 0.6052 (tm-30) REVERT: B 357 PHE cc_start: 0.6507 (p90) cc_final: 0.6189 (p90) REVERT: B 375 MET cc_start: 0.7539 (mtm) cc_final: 0.7187 (mtp) REVERT: B 376 LYS cc_start: 0.8194 (tttt) cc_final: 0.7953 (tptt) REVERT: B 381 LEU cc_start: 0.7663 (mp) cc_final: 0.7402 (mt) REVERT: B 382 MET cc_start: 0.7161 (mtp) cc_final: 0.6783 (mmt) REVERT: B 391 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6797 (pt0) REVERT: B 415 MET cc_start: 0.5831 (mpp) cc_final: 0.5508 (mpp) REVERT: B 519 ASN cc_start: 0.6869 (m-40) cc_final: 0.6508 (m110) REVERT: B 630 ASN cc_start: 0.8801 (p0) cc_final: 0.8550 (p0) REVERT: C 51 MET cc_start: 0.7935 (tpp) cc_final: 0.7317 (tpp) REVERT: C 163 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 225 LEU cc_start: 0.8473 (mt) cc_final: 0.8252 (mt) REVERT: C 234 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7607 (mm-30) outliers start: 2 outliers final: 0 residues processed: 364 average time/residue: 0.1067 time to fit residues: 57.6743 Evaluate side-chains 275 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN A 638 ASN B 11 ASN B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 572 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134427 restraints weight = 23312.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136930 restraints weight = 15542.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138251 restraints weight = 11663.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139703 restraints weight = 9686.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140414 restraints weight = 8320.611| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 14034 Z= 0.135 Angle : 0.602 7.787 18966 Z= 0.311 Chirality : 0.042 0.192 2079 Planarity : 0.004 0.045 2333 Dihedral : 13.049 178.625 2115 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.38 % 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: -1.76 (0.20), residues: 1618 helix: 0.17 (0.19), residues: 746 sheet: -0.77 (0.49), residues: 141 loop : -2.77 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 212 TYR 0.018 0.001 TYR C 11 PHE 0.012 0.001 PHE B 219 TRP 0.017 0.001 TRP A 386 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14034) covalent geometry : angle 0.60154 / 0.31 (18966) hydrogen bonds : bond 0.04424 / 2.87 ( 578) hydrogen bonds : angle 4.84182 / 3.36 ( 1627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4365 (ttp80) cc_final: 0.3424 (mpp-170) REVERT: A 43 GLN cc_start: 0.7999 (tp40) cc_final: 0.7611 (tm-30) REVERT: A 138 LYS cc_start: 0.5894 (mttt) cc_final: 0.5664 (mtmm) REVERT: A 285 GLN cc_start: 0.8450 (pm20) cc_final: 0.7946 (pt0) REVERT: A 291 PHE cc_start: 0.8225 (m-80) cc_final: 0.7377 (m-80) REVERT: A 423 MET cc_start: 0.7820 (mtt) cc_final: 0.7565 (mtt) REVERT: A 492 ASN cc_start: 0.6528 (m-40) cc_final: 0.5903 (p0) REVERT: A 555 MET cc_start: 0.8487 (mmm) cc_final: 0.7703 (mmm) REVERT: A 578 GLU cc_start: 0.7746 (tt0) cc_final: 0.7120 (mt-10) REVERT: A 648 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 77 ASN cc_start: 0.8310 (p0) cc_final: 0.7941 (p0) REVERT: B 138 ARG cc_start: 0.7483 (mtp-110) cc_final: 0.6901 (ttm-80) REVERT: B 157 GLN cc_start: 0.7963 (tm130) cc_final: 0.7729 (tm-30) REVERT: B 178 TRP cc_start: 0.6759 (m-10) cc_final: 0.6529 (m-10) REVERT: B 357 PHE cc_start: 0.6364 (p90) cc_final: 0.6154 (p90) REVERT: B 375 MET cc_start: 0.7608 (mtm) cc_final: 0.7184 (mtp) REVERT: B 381 LEU cc_start: 0.7737 (mp) cc_final: 0.7448 (mt) REVERT: B 382 MET cc_start: 0.7229 (mtp) cc_final: 0.6902 (mmt) REVERT: B 391 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6900 (pt0) REVERT: B 415 MET cc_start: 0.5797 (mpp) cc_final: 0.5578 (mpp) REVERT: B 423 MET cc_start: 0.7693 (mtp) cc_final: 0.7421 (mtm) REVERT: B 450 LEU cc_start: 0.9126 (tp) cc_final: 0.8825 (tp) REVERT: B 682 GLU cc_start: 0.8098 (tt0) cc_final: 0.7529 (tm-30) REVERT: B 686 GLN cc_start: 0.6988 (mm110) cc_final: 0.6513 (mm-40) REVERT: C 9 LYS cc_start: 0.8318 (mttt) cc_final: 0.7776 (ptpt) REVERT: C 163 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7258 (tm-30) REVERT: C 225 LEU cc_start: 0.8362 (mt) cc_final: 0.8074 (mt) REVERT: C 234 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7634 (mm-30) outliers start: 2 outliers final: 1 residues processed: 364 average time/residue: 0.1060 time to fit residues: 57.4387 Evaluate side-chains 291 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 146 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137739 restraints weight = 23066.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139240 restraints weight = 15265.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140389 restraints weight = 12365.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140760 restraints weight = 10667.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141180 restraints weight = 9865.890| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14034 Z= 0.126 Angle : 0.608 8.985 18966 Z= 0.312 Chirality : 0.042 0.197 2079 Planarity : 0.004 0.063 2333 Dihedral : 13.051 178.949 2115 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 0.14 % Allowed : 1.31 % Favored : 98.55 % 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: -1.63 (0.20), residues: 1618 helix: 0.30 (0.19), residues: 746 sheet: -0.75 (0.48), residues: 141 loop : -2.71 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.018 0.001 TYR C 11 PHE 0.017 0.001 PHE A 42 TRP 0.024 0.001 TRP B 178 HIS 0.011 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14034) covalent geometry : angle 0.60793 / 0.31 (18966) hydrogen bonds : bond 0.04321 / 2.80 ( 578) hydrogen bonds : angle 4.74207 / 3.29 ( 1627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4446 (ttp80) cc_final: 0.3456 (mpp-170) REVERT: A 43 GLN cc_start: 0.7934 (tp40) cc_final: 0.7453 (tm-30) REVERT: A 252 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 291 PHE cc_start: 0.8183 (m-80) cc_final: 0.7396 (m-80) REVERT: A 424 CYS cc_start: 0.7897 (t) cc_final: 0.7628 (t) REVERT: A 492 ASN cc_start: 0.6400 (m-40) cc_final: 0.5726 (p0) REVERT: A 555 MET cc_start: 0.8532 (mmm) cc_final: 0.7654 (mmm) REVERT: A 578 GLU cc_start: 0.7621 (tt0) cc_final: 0.7414 (mt-10) REVERT: B 4 ASN cc_start: 0.8161 (t0) cc_final: 0.7294 (t0) REVERT: B 77 ASN cc_start: 0.8195 (p0) cc_final: 0.7769 (p0) REVERT: B 85 VAL cc_start: 0.8463 (t) cc_final: 0.8235 (t) REVERT: B 138 ARG cc_start: 0.7460 (mtp-110) cc_final: 0.6886 (ttm-80) REVERT: B 157 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: B 176 MET cc_start: 0.7023 (mtp) cc_final: 0.6563 (mtm) REVERT: B 178 TRP cc_start: 0.6694 (m-10) cc_final: 0.6479 (m-10) REVERT: B 180 GLU cc_start: 0.6700 (tt0) cc_final: 0.6382 (mp0) REVERT: B 285 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7522 (mttm) REVERT: B 357 PHE cc_start: 0.6466 (p90) cc_final: 0.6006 (p90) REVERT: B 375 MET cc_start: 0.7692 (mtm) cc_final: 0.6481 (mpp) REVERT: B 381 LEU cc_start: 0.7742 (mp) cc_final: 0.7495 (mt) REVERT: B 391 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7039 (pt0) REVERT: B 450 LEU cc_start: 0.9144 (tp) cc_final: 0.8778 (tp) REVERT: B 494 THR cc_start: 0.8419 (p) cc_final: 0.8175 (p) REVERT: B 611 ILE cc_start: 0.8966 (mt) cc_final: 0.8641 (mt) REVERT: B 678 MET cc_start: 0.4395 (ppp) cc_final: 0.4075 (ppp) REVERT: B 682 GLU cc_start: 0.8246 (tt0) cc_final: 0.7694 (tm-30) REVERT: B 686 GLN cc_start: 0.6927 (mm110) cc_final: 0.6426 (mm-40) REVERT: C 9 LYS cc_start: 0.8346 (mttt) cc_final: 0.7800 (ptpt) REVERT: C 10 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7152 (mm-30) REVERT: C 163 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7289 (tm-30) REVERT: C 225 LEU cc_start: 0.8319 (mt) cc_final: 0.8075 (mt) outliers start: 2 outliers final: 0 residues processed: 355 average time/residue: 0.1098 time to fit residues: 57.7613 Evaluate side-chains 283 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 11 ASN B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132549 restraints weight = 23120.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135083 restraints weight = 15452.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136798 restraints weight = 11421.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137989 restraints weight = 9244.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138796 restraints weight = 7924.088| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14034 Z= 0.132 Angle : 0.618 8.551 18966 Z= 0.319 Chirality : 0.042 0.201 2079 Planarity : 0.004 0.048 2333 Dihedral : 13.045 178.794 2115 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 0.21 % Allowed : 1.31 % Favored : 98.48 % 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: -1.50 (0.20), residues: 1618 helix: 0.45 (0.19), residues: 750 sheet: -0.88 (0.47), residues: 141 loop : -2.68 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 26 TYR 0.024 0.001 TYR A 419 PHE 0.021 0.001 PHE A 42 TRP 0.015 0.001 TRP A 386 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14034) covalent geometry : angle 0.61791 / 0.32 (18966) hydrogen bonds : bond 0.04302 / 2.79 ( 578) hydrogen bonds : angle 4.67239 / 3.25 ( 1627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 356 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4391 (ttp80) cc_final: 0.3435 (mpp-170) REVERT: A 43 GLN cc_start: 0.8019 (tp40) cc_final: 0.7418 (tp40) REVERT: A 291 PHE cc_start: 0.8232 (m-80) cc_final: 0.7348 (m-80) REVERT: A 354 GLU cc_start: 0.5751 (tp30) cc_final: 0.5157 (tm-30) REVERT: A 423 MET cc_start: 0.7928 (mtt) cc_final: 0.7513 (mtm) REVERT: A 424 CYS cc_start: 0.7998 (t) cc_final: 0.7656 (t) REVERT: A 492 ASN cc_start: 0.6693 (m-40) cc_final: 0.5874 (p0) REVERT: A 555 MET cc_start: 0.8568 (mmm) cc_final: 0.7918 (mmm) REVERT: A 578 GLU cc_start: 0.7987 (tt0) cc_final: 0.7533 (mt-10) REVERT: B 4 ASN cc_start: 0.8222 (t0) cc_final: 0.7339 (t0) REVERT: B 77 ASN cc_start: 0.8157 (p0) cc_final: 0.7667 (p0) REVERT: B 138 ARG cc_start: 0.7473 (mtp-110) cc_final: 0.6899 (ttm-80) REVERT: B 157 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: B 176 MET cc_start: 0.6798 (mtp) cc_final: 0.6447 (mtm) REVERT: B 310 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7516 (mmmt) REVERT: B 357 PHE cc_start: 0.6436 (p90) cc_final: 0.5921 (p90) REVERT: B 375 MET cc_start: 0.7722 (mtm) cc_final: 0.7201 (mtp) REVERT: B 391 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6904 (pt0) REVERT: B 415 MET cc_start: 0.5665 (mpp) cc_final: 0.5342 (mpp) REVERT: B 450 LEU cc_start: 0.9100 (tp) cc_final: 0.8804 (tp) REVERT: B 604 SER cc_start: 0.8822 (m) cc_final: 0.7890 (t) REVERT: B 675 MET cc_start: 0.5424 (ppp) cc_final: 0.4384 (ppp) REVERT: B 678 MET cc_start: 0.3962 (ppp) cc_final: 0.2553 (mpp) REVERT: B 682 GLU cc_start: 0.8436 (tt0) cc_final: 0.8091 (tm-30) REVERT: B 686 GLN cc_start: 0.6755 (mm110) cc_final: 0.6366 (mm-40) REVERT: C 9 LYS cc_start: 0.8334 (mttt) cc_final: 0.8103 (mttm) REVERT: C 10 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7195 (mm-30) REVERT: C 94 MET cc_start: 0.6733 (tpp) cc_final: 0.6462 (tpp) REVERT: C 163 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 225 LEU cc_start: 0.8163 (mt) cc_final: 0.7914 (mt) REVERT: C 234 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7481 (mm-30) outliers start: 3 outliers final: 1 residues processed: 358 average time/residue: 0.1083 time to fit residues: 57.3028 Evaluate side-chains 273 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 125 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 91 ASN B 11 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131048 restraints weight = 23118.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133412 restraints weight = 15612.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135048 restraints weight = 11749.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136049 restraints weight = 9630.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136929 restraints weight = 8381.433| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14034 Z= 0.168 Angle : 0.652 8.433 18966 Z= 0.337 Chirality : 0.043 0.216 2079 Planarity : 0.004 0.050 2333 Dihedral : 13.051 178.038 2115 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 0.07 % Allowed : 0.97 % Favored : 98.96 % 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: -1.51 (0.20), residues: 1618 helix: 0.51 (0.19), residues: 749 sheet: -1.20 (0.46), residues: 144 loop : -2.69 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 676 TYR 0.022 0.001 TYR A 419 PHE 0.020 0.002 PHE C 35 TRP 0.056 0.002 TRP B 178 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (14034) covalent geometry : angle 0.65161 / 0.34 (18966) hydrogen bonds : bond 0.04593 / 3.00 ( 578) hydrogen bonds : angle 4.69749 / 3.25 ( 1627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4569 (ttp80) cc_final: 0.3612 (mpp-170) REVERT: A 43 GLN cc_start: 0.8043 (tp40) cc_final: 0.7575 (mm-40) REVERT: A 228 LYS cc_start: 0.7595 (pptt) cc_final: 0.7289 (pptt) REVERT: A 229 VAL cc_start: 0.7609 (m) cc_final: 0.7301 (m) REVERT: A 252 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 291 PHE cc_start: 0.8373 (m-80) cc_final: 0.7496 (m-80) REVERT: A 336 SER cc_start: 0.8372 (t) cc_final: 0.7767 (p) REVERT: A 354 GLU cc_start: 0.5720 (tp30) cc_final: 0.5136 (tm-30) REVERT: A 423 MET cc_start: 0.7788 (mtt) cc_final: 0.7435 (mtt) REVERT: A 492 ASN cc_start: 0.7137 (m-40) cc_final: 0.5917 (p0) REVERT: A 555 MET cc_start: 0.8496 (mmm) cc_final: 0.7821 (mmm) REVERT: A 578 GLU cc_start: 0.7951 (tt0) cc_final: 0.7591 (mt-10) REVERT: A 680 CYS cc_start: 0.8201 (t) cc_final: 0.7342 (t) REVERT: B 77 ASN cc_start: 0.8216 (p0) cc_final: 0.7703 (p0) REVERT: B 85 VAL cc_start: 0.8470 (t) cc_final: 0.8258 (t) REVERT: B 138 ARG cc_start: 0.7473 (mtp-110) cc_final: 0.6868 (ttm-80) REVERT: B 157 GLN cc_start: 0.8075 (pp30) cc_final: 0.7590 (pp30) REVERT: B 176 MET cc_start: 0.6959 (mtp) cc_final: 0.6705 (mtm) REVERT: B 310 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7770 (mmmt) REVERT: B 375 MET cc_start: 0.7796 (mtm) cc_final: 0.7266 (mtp) REVERT: B 391 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7044 (pt0) REVERT: B 415 MET cc_start: 0.5596 (mpp) cc_final: 0.5280 (mpp) REVERT: B 450 LEU cc_start: 0.9148 (tp) cc_final: 0.8811 (tp) REVERT: B 460 MET cc_start: 0.8603 (mmt) cc_final: 0.8300 (tpp) REVERT: B 477 ASN cc_start: 0.8035 (m-40) cc_final: 0.7783 (m110) REVERT: B 604 SER cc_start: 0.8877 (m) cc_final: 0.7966 (t) REVERT: B 675 MET cc_start: 0.5512 (ppp) cc_final: 0.4561 (ppp) REVERT: C 9 LYS cc_start: 0.8441 (mttt) cc_final: 0.8202 (mttm) REVERT: C 163 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 186 ILE cc_start: 0.5741 (mp) cc_final: 0.5212 (mm) REVERT: C 225 LEU cc_start: 0.8210 (mt) cc_final: 0.7962 (mt) REVERT: C 234 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7507 (mm-30) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.1050 time to fit residues: 53.5277 Evaluate side-chains 271 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 153 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 113 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 HIS B 11 ASN B 84 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130586 restraints weight = 23274.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132846 restraints weight = 15659.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134609 restraints weight = 11818.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135652 restraints weight = 9641.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136516 restraints weight = 8354.990| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14034 Z= 0.129 Angle : 0.627 8.435 18966 Z= 0.323 Chirality : 0.042 0.207 2079 Planarity : 0.004 0.049 2333 Dihedral : 13.072 179.145 2115 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 0.07 % Allowed : 0.55 % Favored : 99.38 % 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: -1.38 (0.20), residues: 1618 helix: 0.60 (0.19), residues: 752 sheet: -1.23 (0.46), residues: 143 loop : -2.58 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 26 TYR 0.023 0.001 TYR A 419 PHE 0.021 0.001 PHE B 413 TRP 0.022 0.001 TRP B 178 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14034) covalent geometry : angle 0.62708 / 0.32 (18966) hydrogen bonds : bond 0.04315 / 2.81 ( 578) hydrogen bonds : angle 4.57612 / 3.18 ( 1627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4398 (ttp80) cc_final: 0.3457 (mpp-170) REVERT: A 43 GLN cc_start: 0.7815 (tp40) cc_final: 0.7369 (mm-40) REVERT: A 128 MET cc_start: 0.5980 (mpp) cc_final: 0.4938 (mpp) REVERT: A 228 LYS cc_start: 0.7607 (pptt) cc_final: 0.7251 (pptt) REVERT: A 229 VAL cc_start: 0.7476 (m) cc_final: 0.7206 (m) REVERT: A 291 PHE cc_start: 0.8214 (m-80) cc_final: 0.7357 (m-80) REVERT: A 310 LYS cc_start: 0.7336 (pptt) cc_final: 0.6409 (pttt) REVERT: A 336 SER cc_start: 0.8330 (t) cc_final: 0.7708 (p) REVERT: A 354 GLU cc_start: 0.5568 (tp30) cc_final: 0.5087 (tm-30) REVERT: A 555 MET cc_start: 0.8361 (mmm) cc_final: 0.7754 (mmm) REVERT: A 578 GLU cc_start: 0.8006 (tt0) cc_final: 0.7784 (mt-10) REVERT: B 4 ASN cc_start: 0.8218 (t0) cc_final: 0.7490 (t0) REVERT: B 77 ASN cc_start: 0.8222 (p0) cc_final: 0.7704 (p0) REVERT: B 85 VAL cc_start: 0.8400 (t) cc_final: 0.8138 (t) REVERT: B 101 MET cc_start: 0.6974 (pmm) cc_final: 0.6704 (pmm) REVERT: B 138 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.6823 (ttm-80) REVERT: B 157 GLN cc_start: 0.8189 (pp30) cc_final: 0.7745 (pp30) REVERT: B 176 MET cc_start: 0.6944 (mtp) cc_final: 0.6697 (mtm) REVERT: B 259 THR cc_start: 0.8814 (p) cc_final: 0.8136 (t) REVERT: B 280 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7263 (ttmt) REVERT: B 310 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7787 (mmmt) REVERT: B 312 ASN cc_start: 0.8158 (m-40) cc_final: 0.7723 (m-40) REVERT: B 375 MET cc_start: 0.7577 (mtm) cc_final: 0.7105 (mtp) REVERT: B 391 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7024 (pt0) REVERT: B 450 LEU cc_start: 0.9104 (tp) cc_final: 0.8880 (tp) REVERT: B 460 MET cc_start: 0.8491 (mmt) cc_final: 0.8139 (tpp) REVERT: B 467 PHE cc_start: 0.9453 (t80) cc_final: 0.9028 (t80) REVERT: B 604 SER cc_start: 0.8814 (m) cc_final: 0.7917 (t) REVERT: B 675 MET cc_start: 0.5852 (ppp) cc_final: 0.5086 (ppp) REVERT: C 163 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 186 ILE cc_start: 0.5759 (mp) cc_final: 0.5136 (mm) REVERT: C 225 LEU cc_start: 0.8166 (mt) cc_final: 0.7917 (mt) REVERT: C 234 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6993 (mm-30) REVERT: C 236 MET cc_start: 0.7933 (mmp) cc_final: 0.7719 (mmp) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.1044 time to fit residues: 53.1764 Evaluate side-chains 271 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 41 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 HIS ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.160106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133638 restraints weight = 23080.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135993 restraints weight = 15646.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137606 restraints weight = 11833.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138570 restraints weight = 9671.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139563 restraints weight = 8435.086| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14034 Z= 0.134 Angle : 0.630 8.540 18966 Z= 0.326 Chirality : 0.043 0.202 2079 Planarity : 0.004 0.051 2333 Dihedral : 13.070 179.133 2115 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.40 (0.20), residues: 1618 helix: 0.53 (0.19), residues: 756 sheet: -1.18 (0.46), residues: 141 loop : -2.57 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 26 TYR 0.027 0.001 TYR A 419 PHE 0.023 0.001 PHE B 413 TRP 0.071 0.002 TRP B 178 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14034) covalent geometry : angle 0.62952 / 0.33 (18966) hydrogen bonds : bond 0.04427 / 2.94 ( 578) hydrogen bonds : angle 4.58022 / 3.18 ( 1627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4380 (ttp80) cc_final: 0.3435 (mpp-170) REVERT: A 26 ARG cc_start: 0.5243 (mtt180) cc_final: 0.4997 (mtt180) REVERT: A 43 GLN cc_start: 0.7853 (tp40) cc_final: 0.7465 (mm110) REVERT: A 128 MET cc_start: 0.5900 (mpp) cc_final: 0.4834 (mpp) REVERT: A 228 LYS cc_start: 0.7508 (pptt) cc_final: 0.7249 (pptt) REVERT: A 229 VAL cc_start: 0.7516 (m) cc_final: 0.7241 (m) REVERT: A 267 MET cc_start: 0.8008 (mpp) cc_final: 0.7531 (mtm) REVERT: A 291 PHE cc_start: 0.8204 (m-80) cc_final: 0.7404 (m-80) REVERT: A 310 LYS cc_start: 0.7485 (pptt) cc_final: 0.6722 (ptpt) REVERT: A 336 SER cc_start: 0.8411 (t) cc_final: 0.7749 (p) REVERT: A 354 GLU cc_start: 0.5560 (tp30) cc_final: 0.5054 (tm-30) REVERT: A 406 MET cc_start: 0.7151 (ttt) cc_final: 0.6838 (ttt) REVERT: A 424 CYS cc_start: 0.8003 (t) cc_final: 0.7770 (t) REVERT: A 555 MET cc_start: 0.8448 (mmm) cc_final: 0.7755 (mmm) REVERT: B 4 ASN cc_start: 0.8289 (t0) cc_final: 0.7458 (t0) REVERT: B 77 ASN cc_start: 0.8280 (p0) cc_final: 0.7752 (p0) REVERT: B 85 VAL cc_start: 0.8438 (t) cc_final: 0.8175 (t) REVERT: B 101 MET cc_start: 0.6887 (pmm) cc_final: 0.6607 (pmm) REVERT: B 138 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.6803 (ttm-80) REVERT: B 259 THR cc_start: 0.8812 (p) cc_final: 0.8138 (t) REVERT: B 310 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7767 (mmmt) REVERT: B 312 ASN cc_start: 0.8182 (m-40) cc_final: 0.7741 (m-40) REVERT: B 375 MET cc_start: 0.7681 (mtm) cc_final: 0.6553 (mpp) REVERT: B 388 ASP cc_start: 0.8520 (m-30) cc_final: 0.8301 (m-30) REVERT: B 391 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7098 (pt0) REVERT: B 450 LEU cc_start: 0.9101 (tp) cc_final: 0.8828 (tp) REVERT: B 460 MET cc_start: 0.8524 (mmt) cc_final: 0.8183 (tpp) REVERT: B 467 PHE cc_start: 0.9446 (t80) cc_final: 0.9033 (t80) REVERT: B 477 ASN cc_start: 0.8016 (m-40) cc_final: 0.7720 (m110) REVERT: B 523 ASP cc_start: 0.7870 (m-30) cc_final: 0.7591 (m-30) REVERT: B 604 SER cc_start: 0.8837 (m) cc_final: 0.8024 (t) REVERT: B 610 GLU cc_start: 0.6753 (mp0) cc_final: 0.6379 (mt-10) REVERT: B 675 MET cc_start: 0.5738 (ppp) cc_final: 0.5231 (ppp) REVERT: C 94 MET cc_start: 0.6866 (tpp) cc_final: 0.6336 (tpp) REVERT: C 163 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 174 LEU cc_start: 0.7897 (mt) cc_final: 0.7688 (mt) REVERT: C 186 ILE cc_start: 0.5606 (mp) cc_final: 0.5085 (mm) REVERT: C 225 LEU cc_start: 0.8182 (mt) cc_final: 0.7913 (mt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1037 time to fit residues: 53.0046 Evaluate side-chains 277 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 128 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131356 restraints weight = 23317.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133683 restraints weight = 15780.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135323 restraints weight = 11979.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136277 restraints weight = 9779.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137259 restraints weight = 8535.536| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14034 Z= 0.134 Angle : 0.646 11.321 18966 Z= 0.334 Chirality : 0.043 0.208 2079 Planarity : 0.004 0.047 2333 Dihedral : 13.072 179.198 2115 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.43 (0.20), residues: 1618 helix: 0.51 (0.19), residues: 763 sheet: -1.20 (0.46), residues: 141 loop : -2.61 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 212 TYR 0.034 0.001 TYR A 419 PHE 0.019 0.001 PHE B 413 TRP 0.016 0.001 TRP A 386 HIS 0.008 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (14034) covalent geometry : angle 0.64619 / 0.33 (18966) hydrogen bonds : bond 0.04391 / 2.88 ( 578) hydrogen bonds : angle 4.55136 / 3.18 ( 1627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.78 seconds wall clock time: 39 minutes 23.45 seconds (2363.45 seconds total)