Starting phenix.real_space_refine on Sat Sep 12 00:34:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kur_9581/09_2026/6kur_9581_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kur_9581/09_2026/6kur_9581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kur_9581/09_2026/6kur_9581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kur_9581/09_2026/6kur_9581.map" model { file = "/net/cci-nas-00/data/ceres_data/6kur_9581/09_2026/6kur_9581_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kur_9581/09_2026/6kur_9581_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 28 5.49 5 S 109 5.16 5 C 7765 2.51 5 N 2113 2.21 5 O 2369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12384 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5603 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 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: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 2.83, per 1000 atoms: 0.23 Number of scatterers: 12384 At special positions: 0 Unit cell: (110.16, 110.16, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 28 15.00 O 2369 8.00 N 2113 7.00 C 7765 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: 0.98 Conformation dependent library (CDL) restraints added in 535.1 milliseconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 47.2% alpha, 7.7% beta 7 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.700A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.500A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.118A 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: 3.719A 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: 3.645A 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: 3.704A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 620 through 637 removed outlier: 4.119A pdb=" N CYS A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.623A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.715A 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 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.734A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.676A 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 removed outlier: 3.513A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.584A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.672A 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: 3.570A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.788A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.666A 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: 3.573A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.847A 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 425 removed outlier: 3.501A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.568A pdb=" N ALA B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) 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: 3.691A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.682A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 3.807A 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: 3.721A 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 675 through 696 removed outlier: 3.800A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.654A 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: 3.646A 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: 3.942A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.772A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.612A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.690A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.616A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.741A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.621A pdb=" N ARG C 235 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.875A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.624A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.349A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.502A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.481A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.679A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.745A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 153 496 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2031 1.32 - 1.44: 3402 1.44 - 1.57: 7019 1.57 - 1.69: 54 1.69 - 1.82: 181 Bond restraints: 12687 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.376 -0.043 8.40e-03 1.42e+04 2.61e+01 bond pdb=" C LEU B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.89e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.27e-02 6.20e+03 1.84e+01 bond pdb=" C PHE A 563 " pdb=" O PHE A 563 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.43e-02 4.89e+03 7.32e+00 bond pdb=" N ILE A 571 " pdb=" CA ILE A 571 " ideal model delta sigma weight residual 1.461 1.430 0.031 1.23e-02 6.61e+03 6.55e+00 ... (remaining 12682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 16831 2.51 - 5.02: 304 5.02 - 7.53: 37 7.53 - 10.04: 7 10.04 - 12.55: 1 Bond angle restraints: 17180 Sorted by residual: angle pdb=" N ASN A 560 " pdb=" CA ASN A 560 " pdb=" C ASN A 560 " ideal model delta sigma weight residual 113.55 105.32 8.23 1.26e+00 6.30e-01 4.27e+01 angle pdb=" N PHE A 563 " pdb=" CA PHE A 563 " pdb=" C PHE A 563 " ideal model delta sigma weight residual 112.93 104.68 8.25 1.33e+00 5.65e-01 3.85e+01 angle pdb=" C4' U R 9 " pdb=" C3' U R 9 " pdb=" O3' U R 9 " ideal model delta sigma weight residual 109.40 121.95 -12.55 2.10e+00 2.27e-01 3.57e+01 angle pdb=" N MET A 574 " pdb=" CA MET A 574 " pdb=" C MET A 574 " ideal model delta sigma weight residual 111.69 105.79 5.90 1.23e+00 6.61e-01 2.30e+01 angle pdb=" N1 C R 4 " pdb=" C2 C R 4 " pdb=" O2 C R 4 " ideal model delta sigma weight residual 118.90 121.77 -2.87 6.00e-01 2.78e+00 2.28e+01 ... (remaining 17175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 7685 35.18 - 70.36: 118 70.36 - 105.53: 12 105.53 - 140.71: 1 140.71 - 175.89: 1 Dihedral angle restraints: 7817 sinusoidal: 3545 harmonic: 4272 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE A 604 " pdb=" C ILE A 604 " pdb=" N ALA A 605 " pdb=" CA ALA A 605 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1790 0.112 - 0.224: 91 0.224 - 0.336: 4 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C3' U R 9 " pdb=" C4' U R 9 " pdb=" O3' U R 9 " pdb=" C2' U R 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.84e+00 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 2.35 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 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1883 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 628 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ILE A 628 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 628 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 629 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 425 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C GLU A 425 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU A 425 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 426 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 424 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C CYS A 424 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS A 424 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 425 " -0.017 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 316 2.69 - 3.25: 11111 3.25 - 3.80: 17979 3.80 - 4.35: 24423 4.35 - 4.90: 40297 Nonbonded interactions: 94126 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.143 3.120 nonbonded pdb=" OD2 ASP B 523 " pdb=" OH TYR B 560 " model vdw 2.248 3.040 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.251 3.120 nonbonded pdb=" O2' U R 8 " pdb=" OP1 U R 9 " model vdw 2.258 3.040 nonbonded pdb=" O LYS A 460 " pdb=" NZ LYS A 486 " model vdw 2.278 3.120 ... (remaining 94121 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: 0.400 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.060 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12687 Z= 0.235 Angle : 0.802 12.553 17180 Z= 0.494 Chirality : 0.053 0.560 1886 Planarity : 0.006 0.062 2080 Dihedral : 12.356 175.889 5043 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.99 % Favored : 92.87 % Rotamer: Outliers : 1.01 % Allowed : 2.41 % Favored : 96.58 % 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: -4.96 (0.16), residues: 1445 helix: -3.55 (0.11), residues: 642 sheet: -1.69 (0.48), residues: 122 loop : -3.30 (0.19), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 438 TYR 0.020 0.002 TYR B 38 PHE 0.023 0.002 PHE B 420 TRP 0.028 0.003 TRP A 386 HIS 0.009 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.23 (12687) covalent geometry : angle 0.80164 / 0.49 (17180) hydrogen bonds : bond 0.14893 / 9.82 ( 515) hydrogen bonds : angle 9.24728 / 6.35 ( 1430) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 491 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 ASN cc_start: 0.8231 (t0) cc_final: 0.7711 (t0) REVERT: A 516 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 558 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8493 (tm) REVERT: A 568 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8695 (ptt90) REVERT: A 653 LEU cc_start: 0.9177 (mp) cc_final: 0.8890 (mt) REVERT: A 702 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7690 (tttp) REVERT: B 71 THR cc_start: 0.8140 (p) cc_final: 0.7855 (p) REVERT: B 226 ILE cc_start: 0.9133 (mt) cc_final: 0.8876 (pt) REVERT: B 388 ASP cc_start: 0.7501 (m-30) cc_final: 0.7186 (m-30) REVERT: B 554 GLN cc_start: 0.8938 (tp40) cc_final: 0.8585 (tp-100) REVERT: B 675 MET cc_start: 0.5671 (mmm) cc_final: 0.5242 (mmt) REVERT: B 705 ILE cc_start: 0.8832 (pt) cc_final: 0.8609 (mt) REVERT: B 730 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6597 (mm) REVERT: B 736 TYR cc_start: 0.8314 (t80) cc_final: 0.7757 (t80) REVERT: C 180 ASN cc_start: 0.4067 (t0) cc_final: 0.3835 (m-40) REVERT: C 205 VAL cc_start: 0.8948 (t) cc_final: 0.8647 (p) REVERT: C 235 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7727 (ptm-80) outliers start: 13 outliers final: 4 residues processed: 501 average time/residue: 0.1319 time to fit residues: 89.9565 Evaluate side-chains 297 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 290 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 133 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN A 263 HIS A 640 ASN A 657 GLN B 84 ASN B 154 GLN B 157 GLN B 299 GLN B 315 GLN B 436 ASN B 477 ASN B 554 GLN ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS C 141 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124830 restraints weight = 18985.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128808 restraints weight = 9376.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131375 restraints weight = 5950.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132991 restraints weight = 4449.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133780 restraints weight = 3708.477| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12687 Z= 0.145 Angle : 0.657 12.821 17180 Z= 0.340 Chirality : 0.043 0.211 1886 Planarity : 0.005 0.052 2080 Dihedral : 13.709 172.905 2027 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 3.49 % Allowed : 12.66 % Favored : 83.85 % 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: -3.26 (0.19), residues: 1445 helix: -1.53 (0.17), residues: 654 sheet: -0.96 (0.51), residues: 128 loop : -3.10 (0.19), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 741 TYR 0.022 0.001 TYR B 736 PHE 0.020 0.001 PHE B 108 TRP 0.014 0.001 TRP A 357 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (12687) covalent geometry : angle 0.65712 / 0.34 (17180) hydrogen bonds : bond 0.04991 / 3.36 ( 515) hydrogen bonds : angle 5.73166 / 3.98 ( 1430) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8044 (tmm) cc_final: 0.7266 (ttm) REVERT: A 382 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: A 387 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 427 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 442 LYS cc_start: 0.8980 (tttt) cc_final: 0.8498 (ttmm) REVERT: A 453 GLU cc_start: 0.7971 (tp30) cc_final: 0.7738 (tp30) REVERT: A 516 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 568 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8813 (ptt90) REVERT: A 702 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7796 (ttmt) REVERT: B 41 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6099 (tm-30) REVERT: B 45 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7872 (ttm110) REVERT: B 71 THR cc_start: 0.8241 (p) cc_final: 0.8010 (p) REVERT: B 185 LYS cc_start: 0.6011 (ttmt) cc_final: 0.4746 (mttm) REVERT: B 226 ILE cc_start: 0.9151 (mt) cc_final: 0.8855 (pt) REVERT: B 289 SER cc_start: 0.8925 (m) cc_final: 0.8522 (p) REVERT: B 353 MET cc_start: 0.8415 (mmm) cc_final: 0.8201 (mmm) REVERT: B 388 ASP cc_start: 0.8021 (m-30) cc_final: 0.7638 (m-30) REVERT: B 420 PHE cc_start: 0.8852 (m-10) cc_final: 0.8522 (m-10) REVERT: B 423 MET cc_start: 0.8641 (mtm) cc_final: 0.8205 (mtm) REVERT: B 442 LEU cc_start: 0.8921 (tp) cc_final: 0.8601 (mt) REVERT: B 523 ASP cc_start: 0.7837 (m-30) cc_final: 0.7377 (m-30) REVERT: B 675 MET cc_start: 0.5326 (mmm) cc_final: 0.4838 (mmt) REVERT: B 705 ILE cc_start: 0.8875 (pt) cc_final: 0.8637 (mt) REVERT: B 725 GLN cc_start: 0.7613 (mt0) cc_final: 0.7141 (pt0) REVERT: C 242 LEU cc_start: 0.6264 (tt) cc_final: 0.5426 (tt) outliers start: 45 outliers final: 27 residues processed: 322 average time/residue: 0.1059 time to fit residues: 49.3431 Evaluate side-chains 291 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 260 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 70 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 130 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 312 ASN B 572 HIS C 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118725 restraints weight = 19347.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122308 restraints weight = 9949.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124725 restraints weight = 6419.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126287 restraints weight = 4799.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127268 restraints weight = 3965.937| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12687 Z= 0.136 Angle : 0.601 8.568 17180 Z= 0.311 Chirality : 0.043 0.181 1886 Planarity : 0.004 0.058 2080 Dihedral : 13.407 172.249 2010 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 3.03 % Allowed : 14.91 % Favored : 82.07 % 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: -2.45 (0.20), residues: 1445 helix: -0.65 (0.19), residues: 661 sheet: -0.40 (0.55), residues: 116 loop : -2.94 (0.20), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 741 TYR 0.010 0.001 TYR B 692 PHE 0.020 0.001 PHE B 122 TRP 0.013 0.001 TRP A 357 HIS 0.005 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12687) covalent geometry : angle 0.60146 / 0.31 (17180) hydrogen bonds : bond 0.04532 / 3.07 ( 515) hydrogen bonds : angle 5.15308 / 3.61 ( 1430) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8006 (mtt) cc_final: 0.7591 (mtm) REVERT: A 382 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: A 425 GLU cc_start: 0.8082 (tp30) cc_final: 0.7863 (mm-30) REVERT: A 427 LEU cc_start: 0.8822 (tt) cc_final: 0.8508 (tt) REVERT: A 504 GLU cc_start: 0.7757 (mp0) cc_final: 0.7533 (mp0) REVERT: A 568 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8842 (ptt90) REVERT: A 623 LEU cc_start: 0.8881 (tp) cc_final: 0.8614 (tt) REVERT: A 702 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7978 (tttp) REVERT: B 41 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 71 THR cc_start: 0.8248 (p) cc_final: 0.7944 (p) REVERT: B 93 LEU cc_start: 0.9116 (mt) cc_final: 0.8901 (tp) REVERT: B 140 MET cc_start: 0.7299 (mtt) cc_final: 0.7093 (mtp) REVERT: B 226 ILE cc_start: 0.9169 (mt) cc_final: 0.8833 (pt) REVERT: B 266 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 289 SER cc_start: 0.8925 (m) cc_final: 0.8481 (p) REVERT: B 323 MET cc_start: 0.7785 (ttp) cc_final: 0.7360 (ttp) REVERT: B 388 ASP cc_start: 0.8123 (m-30) cc_final: 0.7659 (m-30) REVERT: B 423 MET cc_start: 0.8641 (mtm) cc_final: 0.8128 (mtm) REVERT: B 442 LEU cc_start: 0.8851 (tp) cc_final: 0.8574 (mt) REVERT: B 489 GLU cc_start: 0.7178 (pm20) cc_final: 0.6825 (pm20) REVERT: B 496 MET cc_start: 0.8581 (mtm) cc_final: 0.8257 (mtm) REVERT: B 518 MET cc_start: 0.6830 (tpt) cc_final: 0.6449 (tpt) REVERT: B 523 ASP cc_start: 0.7999 (m-30) cc_final: 0.7455 (m-30) REVERT: B 528 MET cc_start: 0.8193 (mtp) cc_final: 0.7853 (mtm) REVERT: B 675 MET cc_start: 0.4995 (mmm) cc_final: 0.4529 (mmt) REVERT: B 705 ILE cc_start: 0.8896 (pt) cc_final: 0.8673 (mt) REVERT: C 44 GLU cc_start: 0.6511 (tp30) cc_final: 0.6286 (tp30) REVERT: C 180 ASN cc_start: 0.5476 (t0) cc_final: 0.5208 (m-40) REVERT: C 235 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7819 (ptt90) outliers start: 39 outliers final: 27 residues processed: 285 average time/residue: 0.1058 time to fit residues: 43.5199 Evaluate side-chains 273 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 128 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 563 HIS ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114337 restraints weight = 19235.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117986 restraints weight = 10097.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120388 restraints weight = 6596.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121897 restraints weight = 4998.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122848 restraints weight = 4190.497| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12687 Z= 0.144 Angle : 0.586 10.036 17180 Z= 0.301 Chirality : 0.042 0.169 1886 Planarity : 0.004 0.050 2080 Dihedral : 13.352 171.585 2010 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 3.65 % Allowed : 14.67 % Favored : 81.68 % 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: -1.94 (0.21), residues: 1445 helix: -0.15 (0.20), residues: 667 sheet: -0.16 (0.56), residues: 106 loop : -2.75 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 578 TYR 0.012 0.001 TYR B 736 PHE 0.022 0.001 PHE B 122 TRP 0.014 0.001 TRP A 386 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (12687) covalent geometry : angle 0.58620 / 0.30 (17180) hydrogen bonds : bond 0.04452 / 3.03 ( 515) hydrogen bonds : angle 4.75889 / 3.33 ( 1430) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.7948 (mtt) cc_final: 0.7617 (mtm) REVERT: A 382 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: A 387 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8577 (mm) REVERT: A 425 GLU cc_start: 0.7981 (tp30) cc_final: 0.7752 (mm-30) REVERT: A 427 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 568 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8798 (ptt90) REVERT: A 623 LEU cc_start: 0.8971 (tp) cc_final: 0.8690 (tt) REVERT: A 702 LYS cc_start: 0.8255 (tmtt) cc_final: 0.8022 (tttp) REVERT: B 71 THR cc_start: 0.8222 (p) cc_final: 0.7943 (p) REVERT: B 147 GLN cc_start: 0.8546 (mm110) cc_final: 0.8180 (mm110) REVERT: B 266 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 323 MET cc_start: 0.7718 (ttp) cc_final: 0.7515 (ttp) REVERT: B 335 MET cc_start: 0.7840 (tpp) cc_final: 0.7613 (tpp) REVERT: B 388 ASP cc_start: 0.8148 (m-30) cc_final: 0.7670 (m-30) REVERT: B 423 MET cc_start: 0.8633 (mtm) cc_final: 0.8213 (mtm) REVERT: B 442 LEU cc_start: 0.8804 (tp) cc_final: 0.8580 (mt) REVERT: B 489 GLU cc_start: 0.7069 (pm20) cc_final: 0.6768 (pm20) REVERT: B 523 ASP cc_start: 0.8115 (m-30) cc_final: 0.7529 (m-30) REVERT: B 578 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8384 (ttm110) REVERT: B 705 ILE cc_start: 0.8904 (pt) cc_final: 0.8694 (mt) REVERT: B 725 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6566 (pt0) REVERT: C 180 ASN cc_start: 0.5158 (t0) cc_final: 0.4909 (m-40) REVERT: C 217 GLN cc_start: 0.7908 (tt0) cc_final: 0.7509 (mt0) outliers start: 47 outliers final: 31 residues processed: 284 average time/residue: 0.1106 time to fit residues: 45.6412 Evaluate side-chains 270 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111566 restraints weight = 19505.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115098 restraints weight = 10148.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117483 restraints weight = 6632.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119006 restraints weight = 5006.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119878 restraints weight = 4178.817| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12687 Z= 0.157 Angle : 0.595 10.956 17180 Z= 0.306 Chirality : 0.043 0.166 1886 Planarity : 0.004 0.055 2080 Dihedral : 13.333 171.198 2010 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 3.34 % Allowed : 15.53 % Favored : 81.13 % 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: -1.71 (0.21), residues: 1445 helix: 0.10 (0.20), residues: 662 sheet: -0.07 (0.58), residues: 100 loop : -2.65 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.012 0.001 TYR B 736 PHE 0.023 0.001 PHE B 122 TRP 0.021 0.002 TRP A 357 HIS 0.005 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (12687) covalent geometry : angle 0.59477 / 0.31 (17180) hydrogen bonds : bond 0.04513 / 3.07 ( 515) hydrogen bonds : angle 4.60817 / 3.25 ( 1430) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.567 Fit side-chains REVERT: A 196 MET cc_start: 0.8275 (tmm) cc_final: 0.7625 (tmm) REVERT: A 297 MET cc_start: 0.8203 (mtt) cc_final: 0.7923 (mtm) REVERT: A 382 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: A 387 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8657 (mm) REVERT: A 425 GLU cc_start: 0.8031 (tp30) cc_final: 0.7707 (mm-30) REVERT: A 426 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 427 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 568 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8823 (ptt90) REVERT: A 654 MET cc_start: 0.8909 (tpp) cc_final: 0.8697 (tpp) REVERT: A 702 LYS cc_start: 0.8273 (tmtt) cc_final: 0.8026 (ttpt) REVERT: B 41 GLU cc_start: 0.7730 (tm-30) cc_final: 0.6509 (tm-30) REVERT: B 71 THR cc_start: 0.8440 (p) cc_final: 0.8139 (p) REVERT: B 266 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 388 ASP cc_start: 0.8153 (m-30) cc_final: 0.7685 (m-30) REVERT: B 442 LEU cc_start: 0.8836 (tp) cc_final: 0.8589 (mt) REVERT: B 523 ASP cc_start: 0.8179 (m-30) cc_final: 0.7630 (m-30) REVERT: B 578 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8224 (mtp85) REVERT: B 705 ILE cc_start: 0.8953 (pt) cc_final: 0.8715 (mt) REVERT: B 725 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6451 (pt0) REVERT: C 217 GLN cc_start: 0.7941 (tt0) cc_final: 0.7703 (mt0) REVERT: C 235 ARG cc_start: 0.8504 (ptm160) cc_final: 0.8300 (ptt90) outliers start: 43 outliers final: 33 residues processed: 272 average time/residue: 0.1099 time to fit residues: 43.6644 Evaluate side-chains 270 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 106 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 48 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112689 restraints weight = 19413.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116154 restraints weight = 10107.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118483 restraints weight = 6607.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120006 restraints weight = 4981.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120874 restraints weight = 4144.829| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12687 Z= 0.139 Angle : 0.597 10.763 17180 Z= 0.302 Chirality : 0.043 0.208 1886 Planarity : 0.004 0.055 2080 Dihedral : 13.304 171.166 2010 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 3.11 % Allowed : 16.23 % Favored : 80.67 % 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: -1.54 (0.21), residues: 1445 helix: 0.25 (0.20), residues: 665 sheet: -0.09 (0.57), residues: 100 loop : -2.56 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 45 TYR 0.016 0.001 TYR B 560 PHE 0.023 0.001 PHE B 122 TRP 0.017 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (12687) covalent geometry : angle 0.59709 / 0.30 (17180) hydrogen bonds : bond 0.04342 / 2.94 ( 515) hydrogen bonds : angle 4.55989 / 3.20 ( 1430) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.8098 (mtt) cc_final: 0.7852 (mtm) REVERT: A 382 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: A 387 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 427 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 654 MET cc_start: 0.8968 (tpp) cc_final: 0.8755 (tpp) REVERT: A 702 LYS cc_start: 0.8318 (tmtt) cc_final: 0.8089 (tttp) REVERT: B 41 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 71 THR cc_start: 0.8408 (p) cc_final: 0.8103 (p) REVERT: B 147 GLN cc_start: 0.8498 (mm110) cc_final: 0.8142 (mm110) REVERT: B 148 LEU cc_start: 0.9164 (mp) cc_final: 0.8887 (mp) REVERT: B 266 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7924 (mm-30) REVERT: B 388 ASP cc_start: 0.8191 (m-30) cc_final: 0.7698 (m-30) REVERT: B 523 ASP cc_start: 0.8077 (m-30) cc_final: 0.7488 (m-30) REVERT: B 578 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8263 (mtp85) REVERT: B 705 ILE cc_start: 0.8941 (pt) cc_final: 0.8723 (mt) outliers start: 40 outliers final: 31 residues processed: 264 average time/residue: 0.1129 time to fit residues: 43.8125 Evaluate side-chains 269 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN B 554 GLN ** B 725 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.139592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110226 restraints weight = 19357.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113748 restraints weight = 10142.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116076 restraints weight = 6641.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117592 restraints weight = 5058.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118558 restraints weight = 4241.586| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12687 Z= 0.149 Angle : 0.597 11.666 17180 Z= 0.303 Chirality : 0.043 0.164 1886 Planarity : 0.004 0.051 2080 Dihedral : 13.235 170.963 2006 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.06 % Favored : 92.87 % Rotamer: Outliers : 3.18 % Allowed : 16.61 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.21), residues: 1445 helix: 0.39 (0.20), residues: 665 sheet: -0.05 (0.58), residues: 100 loop : -2.53 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 133 TYR 0.012 0.001 TYR C 11 PHE 0.024 0.002 PHE B 122 TRP 0.014 0.001 TRP A 386 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12687) covalent geometry : angle 0.59737 / 0.30 (17180) hydrogen bonds : bond 0.04367 / 2.97 ( 515) hydrogen bonds : angle 4.48245 / 3.15 ( 1430) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.531 Fit side-chains REVERT: A 196 MET cc_start: 0.8267 (tmm) cc_final: 0.7679 (tmm) REVERT: A 382 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: A 387 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 425 GLU cc_start: 0.8173 (tp30) cc_final: 0.7722 (mm-30) REVERT: A 426 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 427 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 622 ASP cc_start: 0.8152 (t70) cc_final: 0.7595 (t70) REVERT: A 702 LYS cc_start: 0.8330 (tmtt) cc_final: 0.8067 (ttpt) REVERT: B 41 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 71 THR cc_start: 0.8415 (p) cc_final: 0.8102 (p) REVERT: B 147 GLN cc_start: 0.8435 (mm110) cc_final: 0.8195 (mm110) REVERT: B 335 MET cc_start: 0.8033 (tpp) cc_final: 0.7702 (tpp) REVERT: B 388 ASP cc_start: 0.8156 (m-30) cc_final: 0.7862 (m-30) REVERT: B 489 GLU cc_start: 0.7108 (pm20) cc_final: 0.6734 (pm20) REVERT: B 523 ASP cc_start: 0.8098 (m-30) cc_final: 0.7556 (m-30) REVERT: B 705 ILE cc_start: 0.8948 (pt) cc_final: 0.8730 (mt) REVERT: C 235 ARG cc_start: 0.8128 (ptt90) cc_final: 0.7636 (ptt90) outliers start: 41 outliers final: 33 residues processed: 266 average time/residue: 0.1136 time to fit residues: 44.0897 Evaluate side-chains 265 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 725 GLN C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108287 restraints weight = 19313.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111729 restraints weight = 10187.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113967 restraints weight = 6752.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115440 restraints weight = 5190.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116407 restraints weight = 4378.933| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12687 Z= 0.186 Angle : 0.650 12.612 17180 Z= 0.329 Chirality : 0.044 0.167 1886 Planarity : 0.004 0.068 2080 Dihedral : 13.266 170.647 2006 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 3.34 % Allowed : 17.08 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.21), residues: 1445 helix: 0.36 (0.20), residues: 666 sheet: -0.26 (0.56), residues: 102 loop : -2.50 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 578 TYR 0.012 0.001 TYR C 11 PHE 0.025 0.002 PHE B 108 TRP 0.017 0.002 TRP B 178 HIS 0.006 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (12687) covalent geometry : angle 0.65038 / 0.33 (17180) hydrogen bonds : bond 0.04611 / 3.13 ( 515) hydrogen bonds : angle 4.49768 / 3.16 ( 1430) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.513 Fit side-chains REVERT: A 196 MET cc_start: 0.8317 (tmm) cc_final: 0.7682 (tmm) REVERT: A 382 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: A 387 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 425 GLU cc_start: 0.8218 (tp30) cc_final: 0.7873 (mm-30) REVERT: A 426 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 427 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 622 ASP cc_start: 0.8285 (t70) cc_final: 0.7633 (t0) REVERT: A 702 LYS cc_start: 0.8366 (tmtt) cc_final: 0.8081 (ttpt) REVERT: B 41 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7031 (tm-30) REVERT: B 71 THR cc_start: 0.8434 (p) cc_final: 0.8119 (p) REVERT: B 147 GLN cc_start: 0.8380 (mm110) cc_final: 0.8124 (mm110) REVERT: B 148 LEU cc_start: 0.9174 (mp) cc_final: 0.8854 (mp) REVERT: B 266 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 388 ASP cc_start: 0.8200 (m-30) cc_final: 0.7905 (m-30) REVERT: B 442 LEU cc_start: 0.8862 (tp) cc_final: 0.8606 (mt) REVERT: B 523 ASP cc_start: 0.8013 (m-30) cc_final: 0.7601 (m-30) REVERT: B 578 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8253 (mtp85) REVERT: B 705 ILE cc_start: 0.8953 (pt) cc_final: 0.8702 (mt) REVERT: C 38 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7528 (m100) REVERT: C 64 ASN cc_start: 0.8069 (t0) cc_final: 0.7865 (t0) REVERT: C 218 PHE cc_start: 0.8278 (m-10) cc_final: 0.7861 (m-80) REVERT: C 235 ARG cc_start: 0.8083 (ptt90) cc_final: 0.7617 (ptt90) outliers start: 43 outliers final: 34 residues processed: 262 average time/residue: 0.1159 time to fit residues: 44.3017 Evaluate side-chains 262 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 133 optimal weight: 0.0170 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 98 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111537 restraints weight = 19153.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115111 restraints weight = 9924.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117457 restraints weight = 6485.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118939 restraints weight = 4924.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119891 restraints weight = 4146.661| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12687 Z= 0.115 Angle : 0.606 11.029 17180 Z= 0.306 Chirality : 0.041 0.157 1886 Planarity : 0.004 0.051 2080 Dihedral : 13.186 170.663 2006 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 2.48 % Allowed : 17.93 % Favored : 79.58 % 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: -1.21 (0.22), residues: 1445 helix: 0.56 (0.20), residues: 667 sheet: -0.08 (0.57), residues: 98 loop : -2.42 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 578 TYR 0.013 0.001 TYR B 560 PHE 0.022 0.001 PHE B 122 TRP 0.030 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (12687) covalent geometry : angle 0.60578 / 0.31 (17180) hydrogen bonds : bond 0.04007 / 2.71 ( 515) hydrogen bonds : angle 4.31950 / 3.03 ( 1430) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.507 Fit side-chains REVERT: A 196 MET cc_start: 0.8287 (tmm) cc_final: 0.7642 (tmm) REVERT: A 382 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: A 425 GLU cc_start: 0.8133 (tp30) cc_final: 0.7686 (mm-30) REVERT: A 427 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8620 (tt) REVERT: A 497 MET cc_start: 0.7485 (mpp) cc_final: 0.7257 (mtm) REVERT: A 622 ASP cc_start: 0.8142 (t70) cc_final: 0.7528 (t70) REVERT: A 702 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7900 (ttpp) REVERT: B 41 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7127 (tm-30) REVERT: B 71 THR cc_start: 0.8413 (p) cc_final: 0.8101 (p) REVERT: B 147 GLN cc_start: 0.8276 (mm110) cc_final: 0.8013 (mm110) REVERT: B 148 LEU cc_start: 0.9158 (mp) cc_final: 0.8820 (mp) REVERT: B 266 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 335 MET cc_start: 0.8057 (tpp) cc_final: 0.7759 (tpp) REVERT: B 388 ASP cc_start: 0.8182 (m-30) cc_final: 0.7879 (m-30) REVERT: B 489 GLU cc_start: 0.6920 (pm20) cc_final: 0.6439 (pm20) REVERT: B 578 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8226 (mtp85) REVERT: C 38 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.7349 (m100) REVERT: C 235 ARG cc_start: 0.8098 (ptt90) cc_final: 0.7625 (ptt90) outliers start: 32 outliers final: 25 residues processed: 260 average time/residue: 0.1143 time to fit residues: 43.5200 Evaluate side-chains 256 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 0.0370 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111183 restraints weight = 19358.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114798 restraints weight = 9951.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117132 restraints weight = 6460.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118622 restraints weight = 4899.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119621 restraints weight = 4112.708| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12687 Z= 0.122 Angle : 0.615 10.877 17180 Z= 0.307 Chirality : 0.042 0.184 1886 Planarity : 0.004 0.049 2080 Dihedral : 13.155 170.195 2006 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 2.33 % Allowed : 18.48 % Favored : 79.19 % 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: -1.11 (0.22), residues: 1445 helix: 0.68 (0.20), residues: 661 sheet: -0.04 (0.58), residues: 98 loop : -2.38 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 578 TYR 0.011 0.001 TYR B 560 PHE 0.021 0.001 PHE A 292 TRP 0.023 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12687) covalent geometry : angle 0.61510 / 0.31 (17180) hydrogen bonds : bond 0.03988 / 2.70 ( 515) hydrogen bonds : angle 4.28338 / 3.00 ( 1430) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.486 Fit side-chains REVERT: A 196 MET cc_start: 0.8345 (tmm) cc_final: 0.7651 (tmm) REVERT: A 382 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: A 425 GLU cc_start: 0.8162 (tp30) cc_final: 0.7889 (mm-30) REVERT: A 426 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 427 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8642 (tt) REVERT: A 622 ASP cc_start: 0.8177 (t70) cc_final: 0.7484 (t0) REVERT: A 702 LYS cc_start: 0.8330 (tmtt) cc_final: 0.8042 (ttpt) REVERT: B 41 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 71 THR cc_start: 0.8432 (p) cc_final: 0.8119 (p) REVERT: B 148 LEU cc_start: 0.9159 (mp) cc_final: 0.8791 (mp) REVERT: B 184 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6543 (pttt) REVERT: B 335 MET cc_start: 0.8036 (tpp) cc_final: 0.7740 (tpp) REVERT: B 388 ASP cc_start: 0.8187 (m-30) cc_final: 0.7901 (m-30) REVERT: B 489 GLU cc_start: 0.7044 (pm20) cc_final: 0.6510 (pm20) REVERT: B 578 ARG cc_start: 0.8584 (ttm110) cc_final: 0.8244 (mtp85) REVERT: B 740 LYS cc_start: 0.7825 (pttt) cc_final: 0.7503 (pttm) REVERT: C 38 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7433 (m100) REVERT: C 235 ARG cc_start: 0.8075 (ptt90) cc_final: 0.7660 (ptt90) outliers start: 30 outliers final: 23 residues processed: 244 average time/residue: 0.1128 time to fit residues: 40.4785 Evaluate side-chains 248 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111336 restraints weight = 19359.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114928 restraints weight = 9992.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117217 restraints weight = 6494.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118809 restraints weight = 4935.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119626 restraints weight = 4115.043| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12687 Z= 0.122 Angle : 0.623 10.698 17180 Z= 0.312 Chirality : 0.042 0.166 1886 Planarity : 0.004 0.051 2080 Dihedral : 13.134 169.732 2006 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.43 % Rotamer: Outliers : 2.17 % Allowed : 18.56 % Favored : 79.27 % 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: -1.02 (0.22), residues: 1445 helix: 0.70 (0.20), residues: 665 sheet: -0.17 (0.55), residues: 108 loop : -2.28 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 578 TYR 0.012 0.001 TYR C 11 PHE 0.022 0.001 PHE C 212 TRP 0.037 0.002 TRP A 357 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12687) covalent geometry : angle 0.62302 / 0.31 (17180) hydrogen bonds : bond 0.03959 / 2.69 ( 515) hydrogen bonds : angle 4.25878 / 2.98 ( 1430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.64 seconds wall clock time: 38 minutes 57.00 seconds (2337.00 seconds total)