Starting phenix.real_space_refine on Wed Mar 4 09:36:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kur_9581/03_2026/6kur_9581_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kur_9581/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kur_9581/03_2026/6kur_9581_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kur_9581/03_2026/6kur_9581_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kur_9581/03_2026/6kur_9581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kur_9581/03_2026/6kur_9581.map" } 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-dev-5986/lib/python3.9/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: 2.81, 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: 0.93 Conformation dependent library (CDL) restraints added in 513.2 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: 1.50 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: 1.87 Time building geometry restraints manager: 1.33 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: 16858 2.51 - 5.02: 277 5.02 - 7.53: 37 7.53 - 10.04: 7 10.04 - 12.55: 1 Bond angle restraints: 17180 Sorted by residual: 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 1.50e+00 4.44e-01 7.00e+01 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=" 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=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.66 -5.09 1.25e+00 6.40e-01 1.66e+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: 1808 0.112 - 0.224: 73 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.040 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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= 0.227 Angle : 0.788 12.553 17180 Z= 0.445 Chirality : 0.052 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 covalent geometry : bond 0.00403 (12687) covalent geometry : angle 0.78774 (17180) hydrogen bonds : bond 0.14893 ( 515) hydrogen bonds : angle 9.24728 ( 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 : 0.503 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: 0.1349 time to fit residues: 91.0242 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 : 0.405 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 263 HIS A 640 ASN A 657 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 299 GLN B 315 GLN B 436 ASN B 477 ASN B 554 GLN B 572 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS C 141 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125380 restraints weight = 18943.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129457 restraints weight = 9356.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131969 restraints weight = 5866.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133590 restraints weight = 4376.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134569 restraints weight = 3624.963| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12687 Z= 0.121 Angle : 0.602 9.596 17180 Z= 0.311 Chirality : 0.042 0.155 1886 Planarity : 0.005 0.053 2080 Dihedral : 13.512 169.071 2027 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 2.95 % Allowed : 13.04 % Favored : 84.01 % 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: -2.96 (0.19), residues: 1445 helix: -1.19 (0.18), residues: 663 sheet: -0.59 (0.54), residues: 116 loop : -3.09 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 741 TYR 0.015 0.001 TYR B 736 PHE 0.023 0.001 PHE C 175 TRP 0.014 0.001 TRP A 357 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00261 (12687) covalent geometry : angle 0.60159 (17180) hydrogen bonds : bond 0.04415 ( 515) hydrogen bonds : angle 5.14331 ( 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 341 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8117 (tmm) cc_final: 0.7468 (ttm) REVERT: A 207 ASN cc_start: 0.8742 (p0) cc_final: 0.8304 (p0) REVERT: A 382 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: A 387 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8668 (mm) REVERT: A 427 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8620 (tt) REVERT: A 502 THR cc_start: 0.8468 (p) cc_final: 0.8236 (p) REVERT: A 568 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8659 (ptt90) REVERT: A 623 LEU cc_start: 0.8648 (tp) cc_final: 0.8377 (tt) REVERT: A 702 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7965 (tttp) REVERT: B 41 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6768 (tm-30) REVERT: B 45 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7632 (mtm180) REVERT: B 71 THR cc_start: 0.8180 (p) cc_final: 0.7929 (p) REVERT: B 140 MET cc_start: 0.7274 (mtt) cc_final: 0.7049 (mtp) REVERT: B 226 ILE cc_start: 0.9173 (mt) cc_final: 0.8913 (pt) REVERT: B 289 SER cc_start: 0.8911 (m) cc_final: 0.8418 (p) REVERT: B 339 CYS cc_start: 0.8501 (m) cc_final: 0.8229 (m) REVERT: B 388 ASP cc_start: 0.8011 (m-30) cc_final: 0.7611 (m-30) REVERT: B 423 MET cc_start: 0.8542 (mtm) cc_final: 0.7954 (mtm) REVERT: B 442 LEU cc_start: 0.8877 (tp) cc_final: 0.8545 (mt) REVERT: B 523 ASP cc_start: 0.7795 (m-30) cc_final: 0.7365 (m-30) REVERT: B 705 ILE cc_start: 0.8912 (pt) cc_final: 0.8676 (mt) outliers start: 38 outliers final: 19 residues processed: 323 average time/residue: 0.1156 time to fit residues: 52.7327 Evaluate side-chains 277 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 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 679 GLU 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 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 730 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: 2.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 39 optimal weight: 7.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 638 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 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 = 0.3736 r_free = 0.3736 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116926 restraints weight = 19306.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120562 restraints weight = 9947.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123001 restraints weight = 6469.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124556 restraints weight = 4856.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125540 restraints weight = 4047.342| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12687 Z= 0.117 Angle : 0.568 8.722 17180 Z= 0.290 Chirality : 0.041 0.146 1886 Planarity : 0.004 0.060 2080 Dihedral : 13.252 168.748 2012 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 3.34 % Allowed : 14.91 % Favored : 81.75 % 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: -1.96 (0.21), residues: 1445 helix: -0.15 (0.20), residues: 664 sheet: -0.20 (0.57), residues: 106 loop : -2.76 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 578 TYR 0.008 0.001 TYR B 38 PHE 0.015 0.001 PHE A 632 TRP 0.012 0.001 TRP A 386 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00254 (12687) covalent geometry : angle 0.56828 (17180) hydrogen bonds : bond 0.04108 ( 515) hydrogen bonds : angle 4.54010 ( 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 313 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7846 (m-30) cc_final: 0.7229 (p0) REVERT: A 382 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: A 426 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 427 LEU cc_start: 0.8869 (tt) cc_final: 0.8576 (tt) REVERT: A 504 GLU cc_start: 0.7819 (mp0) cc_final: 0.7377 (mp0) REVERT: A 568 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8761 (ptt90) REVERT: A 702 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7824 (ttpp) REVERT: B 41 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6545 (tm-30) REVERT: B 71 THR cc_start: 0.8274 (p) cc_final: 0.7999 (p) REVERT: B 151 ASP cc_start: 0.7857 (t0) cc_final: 0.7560 (t0) REVERT: B 266 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7718 (mm-30) REVERT: B 289 SER cc_start: 0.9059 (m) cc_final: 0.8495 (p) REVERT: B 388 ASP cc_start: 0.8219 (m-30) cc_final: 0.7758 (m-30) REVERT: B 489 GLU cc_start: 0.6920 (pm20) cc_final: 0.6631 (pm20) REVERT: B 523 ASP cc_start: 0.7936 (m-30) cc_final: 0.7365 (m-30) REVERT: C 164 LYS cc_start: 0.9065 (tppt) cc_final: 0.8830 (tppt) REVERT: C 217 GLN cc_start: 0.7964 (tt0) cc_final: 0.7565 (mt0) outliers start: 43 outliers final: 23 residues processed: 296 average time/residue: 0.1083 time to fit residues: 45.9327 Evaluate side-chains 261 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 568 ARG 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 304 ILE Chi-restraints excluded: chain B residue 305 THR 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 730 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 125 LYS 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: 1.9990 chunk 131 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 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 = 0.3676 r_free = 0.3676 target = 0.140860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111777 restraints weight = 19425.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115273 restraints weight = 10029.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117587 restraints weight = 6538.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119082 restraints weight = 4968.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120052 restraints weight = 4155.945| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12687 Z= 0.158 Angle : 0.586 10.536 17180 Z= 0.299 Chirality : 0.043 0.161 1886 Planarity : 0.004 0.063 2080 Dihedral : 13.217 167.736 2012 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 3.34 % Allowed : 15.30 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1445 helix: 0.24 (0.20), residues: 668 sheet: -0.10 (0.56), residues: 106 loop : -2.64 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 578 TYR 0.008 0.001 TYR B 38 PHE 0.014 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 covalent geometry : bond 0.00362 (12687) covalent geometry : angle 0.58559 (17180) hydrogen bonds : bond 0.04301 ( 515) hydrogen bonds : angle 4.46989 ( 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 296 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6520 (ttm) REVERT: A 196 MET cc_start: 0.8295 (tmm) cc_final: 0.7696 (tmm) REVERT: A 339 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8380 (ptt180) REVERT: A 382 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: A 426 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 427 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 622 ASP cc_start: 0.7876 (t70) cc_final: 0.7308 (t0) REVERT: A 653 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9041 (mp) REVERT: A 702 LYS cc_start: 0.8318 (tmtt) cc_final: 0.8114 (tttp) REVERT: B 41 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 71 THR cc_start: 0.8362 (p) cc_final: 0.8071 (p) REVERT: B 148 LEU cc_start: 0.9229 (mp) cc_final: 0.8863 (mp) REVERT: B 151 ASP cc_start: 0.7815 (t0) cc_final: 0.7494 (t0) REVERT: B 222 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8333 (ttm170) REVERT: B 388 ASP cc_start: 0.8184 (m-30) cc_final: 0.7713 (m-30) REVERT: B 412 MET cc_start: 0.6809 (mpp) cc_final: 0.6551 (mpp) REVERT: B 442 LEU cc_start: 0.8833 (tp) cc_final: 0.8496 (mt) REVERT: B 489 GLU cc_start: 0.6859 (pm20) cc_final: 0.6539 (pm20) REVERT: B 523 ASP cc_start: 0.8049 (m-30) cc_final: 0.7526 (m-30) REVERT: B 578 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8168 (mtp85) REVERT: B 615 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: C 164 LYS cc_start: 0.9041 (tppt) cc_final: 0.7948 (tppt) REVERT: C 168 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: C 218 PHE cc_start: 0.8315 (m-10) cc_final: 0.7971 (m-80) outliers start: 43 outliers final: 26 residues processed: 277 average time/residue: 0.1030 time to fit residues: 41.8604 Evaluate side-chains 264 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ARG 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 404 ILE 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 464 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 LYS 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 248 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108695 restraints weight = 19647.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112240 restraints weight = 10141.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114583 restraints weight = 6600.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116080 restraints weight = 5007.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117084 restraints weight = 4198.028| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12687 Z= 0.166 Angle : 0.602 11.398 17180 Z= 0.307 Chirality : 0.043 0.153 1886 Planarity : 0.004 0.067 2080 Dihedral : 13.168 167.330 2006 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 4.19 % Allowed : 15.30 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1445 helix: 0.43 (0.20), residues: 665 sheet: -0.60 (0.54), residues: 116 loop : -2.44 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 131 TYR 0.012 0.001 TYR C 11 PHE 0.016 0.002 PHE B 122 TRP 0.015 0.002 TRP A 386 HIS 0.006 0.002 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00382 (12687) covalent geometry : angle 0.60205 (17180) hydrogen bonds : bond 0.04432 ( 515) hydrogen bonds : angle 4.38662 ( 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 304 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6664 (ttm) REVERT: A 339 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8358 (ptt180) REVERT: A 382 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: A 426 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 427 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8639 (tt) REVERT: A 622 ASP cc_start: 0.7963 (t70) cc_final: 0.7346 (t0) REVERT: A 653 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 702 LYS cc_start: 0.8350 (tmtt) cc_final: 0.8113 (ttpt) REVERT: B 41 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6764 (tm-30) REVERT: B 71 THR cc_start: 0.8307 (p) cc_final: 0.7999 (p) REVERT: B 140 MET cc_start: 0.7571 (mtp) cc_final: 0.7208 (mtt) REVERT: B 148 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8844 (mp) REVERT: B 151 ASP cc_start: 0.7834 (t0) cc_final: 0.7574 (t0) REVERT: B 184 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5871 (pttt) REVERT: B 266 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 388 ASP cc_start: 0.8136 (m-30) cc_final: 0.7858 (m-30) REVERT: B 523 ASP cc_start: 0.7901 (m-30) cc_final: 0.7360 (m-30) REVERT: B 578 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8177 (mtp85) REVERT: B 615 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: B 748 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7657 (mmm160) REVERT: C 10 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6695 (mm-30) REVERT: C 38 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7486 (m100) REVERT: C 164 LYS cc_start: 0.8926 (tppt) cc_final: 0.7840 (tppt) REVERT: C 218 PHE cc_start: 0.8204 (m-10) cc_final: 0.7807 (m-80) outliers start: 54 outliers final: 31 residues processed: 280 average time/residue: 0.1105 time to fit residues: 44.5259 Evaluate side-chains 272 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 339 ARG 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 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 653 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 118 LEU Chi-restraints excluded: chain B residue 148 LEU 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 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR 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 592 ILE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP 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: 0.0040 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.0030 chunk 15 optimal weight: 0.3980 chunk 145 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3694 r_free = 0.3694 target = 0.142684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114393 restraints weight = 19350.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117940 restraints weight = 9933.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120273 restraints weight = 6395.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121787 restraints weight = 4819.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122618 restraints weight = 3999.753| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12687 Z= 0.106 Angle : 0.580 8.735 17180 Z= 0.290 Chirality : 0.041 0.147 1886 Planarity : 0.004 0.069 2080 Dihedral : 13.033 166.297 2006 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 3.42 % Allowed : 16.69 % Favored : 79.89 % 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: -1.16 (0.22), residues: 1445 helix: 0.67 (0.21), residues: 663 sheet: -0.53 (0.55), residues: 110 loop : -2.39 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 131 TYR 0.012 0.001 TYR C 11 PHE 0.022 0.001 PHE B 108 TRP 0.018 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00230 (12687) covalent geometry : angle 0.57967 (17180) hydrogen bonds : bond 0.03712 ( 515) hydrogen bonds : angle 4.18820 ( 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 294 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6433 (ttm) REVERT: A 196 MET cc_start: 0.8247 (tmm) cc_final: 0.7582 (tmm) REVERT: A 339 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8265 (ptt180) REVERT: A 382 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: A 426 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 427 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 584 GLU cc_start: 0.8216 (tp30) cc_final: 0.7667 (tp30) REVERT: A 622 ASP cc_start: 0.8012 (t70) cc_final: 0.7283 (t0) REVERT: A 653 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8794 (mp) REVERT: A 702 LYS cc_start: 0.8311 (tmtt) cc_final: 0.7878 (ttpp) REVERT: B 41 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6753 (tm-30) REVERT: B 45 ARG cc_start: 0.8276 (ttp-170) cc_final: 0.7957 (mtm180) REVERT: B 71 THR cc_start: 0.8313 (p) cc_final: 0.8002 (p) REVERT: B 140 MET cc_start: 0.7360 (mtp) cc_final: 0.7026 (mtt) REVERT: B 148 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 151 ASP cc_start: 0.7799 (t0) cc_final: 0.7506 (t0) REVERT: B 178 TRP cc_start: 0.7718 (m-10) cc_final: 0.7427 (m-10) REVERT: B 184 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5764 (pttt) REVERT: B 388 ASP cc_start: 0.8122 (m-30) cc_final: 0.7861 (m-30) REVERT: B 610 GLU cc_start: 0.8405 (pm20) cc_final: 0.8117 (pm20) REVERT: B 615 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: B 748 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7837 (mmm160) REVERT: C 38 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7564 (m100) REVERT: C 44 GLU cc_start: 0.6023 (tp30) cc_final: 0.5511 (tp30) REVERT: C 50 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7616 (ttp80) REVERT: C 74 PRO cc_start: 0.7808 (Cg_exo) cc_final: 0.7583 (Cg_endo) REVERT: C 164 LYS cc_start: 0.8722 (tppt) cc_final: 0.7796 (tppt) REVERT: C 168 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7273 (mp0) outliers start: 44 outliers final: 24 residues processed: 276 average time/residue: 0.1062 time to fit residues: 42.3747 Evaluate side-chains 267 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET 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 339 ARG 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 464 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 348 ASN 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 615 ASP Chi-restraints excluded: chain C residue 34 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 263 HIS ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109255 restraints weight = 19438.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112653 restraints weight = 10068.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114855 restraints weight = 6582.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116298 restraints weight = 5003.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117113 restraints weight = 4206.620| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12687 Z= 0.171 Angle : 0.631 10.953 17180 Z= 0.319 Chirality : 0.044 0.182 1886 Planarity : 0.004 0.052 2080 Dihedral : 13.190 166.384 2006 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.06 % Favored : 92.87 % Rotamer: Outliers : 3.65 % Allowed : 17.16 % 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: 0.63 (0.20), residues: 668 sheet: -0.70 (0.52), residues: 124 loop : -2.28 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 578 TYR 0.011 0.001 TYR A 549 PHE 0.018 0.002 PHE B 122 TRP 0.016 0.001 TRP A 357 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00393 (12687) covalent geometry : angle 0.63115 (17180) hydrogen bonds : bond 0.04507 ( 515) hydrogen bonds : angle 4.28614 ( 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 276 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6643 (ttm) REVERT: A 339 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8390 (ptt180) REVERT: A 382 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: A 426 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 427 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 622 ASP cc_start: 0.8213 (t70) cc_final: 0.7473 (t0) REVERT: A 653 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 702 LYS cc_start: 0.8354 (tmtt) cc_final: 0.8061 (ttpt) REVERT: B 41 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 71 THR cc_start: 0.8406 (p) cc_final: 0.8100 (p) REVERT: B 140 MET cc_start: 0.7536 (mtp) cc_final: 0.7111 (mtt) REVERT: B 148 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8767 (mp) REVERT: B 151 ASP cc_start: 0.7799 (t0) cc_final: 0.7563 (t0) REVERT: B 178 TRP cc_start: 0.7806 (m-10) cc_final: 0.7568 (m-10) REVERT: B 184 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.6054 (pttt) REVERT: B 248 MET cc_start: 0.7734 (tpp) cc_final: 0.7333 (tpp) REVERT: B 266 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 388 ASP cc_start: 0.8073 (m-30) cc_final: 0.7826 (m-30) REVERT: B 523 ASP cc_start: 0.8009 (m-30) cc_final: 0.7657 (m-30) REVERT: B 578 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8192 (mtp85) REVERT: B 615 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: B 710 MET cc_start: 0.7696 (mmt) cc_final: 0.7178 (tpt) REVERT: B 748 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7798 (mmm160) REVERT: C 38 TRP cc_start: 0.8369 (OUTLIER) cc_final: 0.7573 (m100) REVERT: C 164 LYS cc_start: 0.8770 (tppt) cc_final: 0.7859 (tppt) REVERT: C 168 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7333 (mp0) outliers start: 47 outliers final: 28 residues processed: 253 average time/residue: 0.1042 time to fit residues: 38.3498 Evaluate side-chains 253 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET 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 326 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ARG 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 390 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 653 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 148 LEU 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 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 482 LYS 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 615 ASP Chi-restraints excluded: chain C residue 34 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 0.0030 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** 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 = 0.3660 r_free = 0.3660 target = 0.139901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109709 restraints weight = 19326.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113226 restraints weight = 10106.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115593 restraints weight = 6675.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116930 restraints weight = 5097.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117979 restraints weight = 4332.375| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5046 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 : 0.607 10.394 17180 Z= 0.304 Chirality : 0.042 0.205 1886 Planarity : 0.004 0.048 2080 Dihedral : 13.122 165.650 2006 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 3.26 % Allowed : 17.70 % Favored : 79.04 % 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: -0.96 (0.22), residues: 1445 helix: 0.79 (0.20), residues: 668 sheet: -0.78 (0.51), residues: 123 loop : -2.20 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 578 TYR 0.013 0.001 TYR C 11 PHE 0.025 0.001 PHE B 108 TRP 0.020 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00276 (12687) covalent geometry : angle 0.60685 (17180) hydrogen bonds : bond 0.03980 ( 515) hydrogen bonds : angle 4.16238 ( 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 279 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8266 (tmm) cc_final: 0.7532 (tmm) REVERT: A 339 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8330 (ptt180) REVERT: A 382 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: A 385 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: A 426 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 427 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 622 ASP cc_start: 0.8089 (t70) cc_final: 0.7307 (t0) REVERT: A 702 LYS cc_start: 0.8305 (tmtt) cc_final: 0.8008 (ttpt) REVERT: B 41 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6909 (tm-30) REVERT: B 71 THR cc_start: 0.8437 (p) cc_final: 0.8120 (p) REVERT: B 140 MET cc_start: 0.7402 (mtp) cc_final: 0.7060 (mtt) REVERT: B 148 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 151 ASP cc_start: 0.7839 (t0) cc_final: 0.7551 (t0) REVERT: B 178 TRP cc_start: 0.7733 (m-10) cc_final: 0.7364 (m-10) REVERT: B 184 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6109 (pttt) REVERT: B 248 MET cc_start: 0.7702 (tpp) cc_final: 0.7215 (tpp) REVERT: B 266 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 388 ASP cc_start: 0.8095 (m-30) cc_final: 0.7807 (m-30) REVERT: B 523 ASP cc_start: 0.7875 (m-30) cc_final: 0.7560 (m-30) REVERT: B 578 ARG cc_start: 0.8582 (ttm110) cc_final: 0.8188 (mtp85) REVERT: B 615 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: B 710 MET cc_start: 0.7968 (mmt) cc_final: 0.7410 (tpt) REVERT: B 748 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7763 (mmm160) REVERT: C 38 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7597 (m100) REVERT: C 44 GLU cc_start: 0.6040 (tp30) cc_final: 0.5451 (tp30) REVERT: C 164 LYS cc_start: 0.8755 (tppt) cc_final: 0.7802 (tppt) REVERT: C 168 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 231 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8581 (mm) outliers start: 42 outliers final: 22 residues processed: 262 average time/residue: 0.1057 time to fit residues: 40.4664 Evaluate side-chains 260 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 336 SER Chi-restraints excluded: chain A residue 339 ARG 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 385 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 THR 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 148 LEU 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 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR 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 615 ASP Chi-restraints excluded: chain C residue 34 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 231 ILE 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: 9.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** 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 = 0.3656 r_free = 0.3656 target = 0.139552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109603 restraints weight = 19359.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113174 restraints weight = 10065.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115501 restraints weight = 6585.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117011 restraints weight = 5018.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117867 restraints weight = 4219.259| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5166 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= 0.129 Angle : 0.622 10.676 17180 Z= 0.311 Chirality : 0.043 0.209 1886 Planarity : 0.004 0.047 2080 Dihedral : 13.121 165.492 2006 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 2.72 % Allowed : 18.48 % Favored : 78.80 % 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: -0.86 (0.22), residues: 1445 helix: 0.86 (0.21), residues: 667 sheet: -0.73 (0.51), residues: 123 loop : -2.13 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 578 TYR 0.009 0.001 TYR C 104 PHE 0.022 0.001 PHE B 108 TRP 0.020 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00295 (12687) covalent geometry : angle 0.62194 (17180) hydrogen bonds : bond 0.04002 ( 515) hydrogen bonds : angle 4.13867 ( 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 271 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8251 (tmm) cc_final: 0.7545 (tmm) REVERT: A 221 ASN cc_start: 0.8404 (t0) cc_final: 0.8179 (t0) REVERT: A 222 GLN cc_start: 0.8221 (mm110) cc_final: 0.7870 (mm-40) REVERT: A 339 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8352 (ptt180) REVERT: A 382 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: A 385 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: A 426 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 427 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 622 ASP cc_start: 0.8110 (t70) cc_final: 0.7295 (t70) REVERT: A 702 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7978 (ttpt) REVERT: A 709 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7040 (m-10) REVERT: B 41 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 71 THR cc_start: 0.8476 (p) cc_final: 0.8160 (p) REVERT: B 140 MET cc_start: 0.7413 (mtp) cc_final: 0.7056 (mtt) REVERT: B 148 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8763 (mp) REVERT: B 151 ASP cc_start: 0.7835 (t0) cc_final: 0.7534 (t0) REVERT: B 184 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6192 (pttt) REVERT: B 222 ARG cc_start: 0.8553 (ttm170) cc_final: 0.7616 (ttt180) REVERT: B 248 MET cc_start: 0.7860 (tpp) cc_final: 0.7430 (tpp) REVERT: B 266 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 388 ASP cc_start: 0.8142 (m-30) cc_final: 0.7868 (m-30) REVERT: B 523 ASP cc_start: 0.7852 (m-30) cc_final: 0.7351 (m-30) REVERT: B 578 ARG cc_start: 0.8614 (ttm110) cc_final: 0.8248 (mtp85) REVERT: B 615 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: B 710 MET cc_start: 0.7956 (mmt) cc_final: 0.7395 (tpt) REVERT: B 748 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7665 (mmm160) REVERT: C 38 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7584 (m100) REVERT: C 164 LYS cc_start: 0.8747 (tppt) cc_final: 0.7808 (tppt) REVERT: C 168 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: C 231 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (mm) outliers start: 35 outliers final: 20 residues processed: 257 average time/residue: 0.1074 time to fit residues: 40.0742 Evaluate side-chains 257 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 336 SER Chi-restraints excluded: chain A residue 339 ARG 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 385 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU 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 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR 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 C residue 34 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 231 ILE 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: 5.9990 chunk 48 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN ** B 84 ASN ** 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 = 0.3682 r_free = 0.3682 target = 0.141930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113166 restraints weight = 19438.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116699 restraints weight = 10011.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119027 restraints weight = 6500.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120399 restraints weight = 4911.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121421 restraints weight = 4127.847| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12687 Z= 0.113 Angle : 0.609 8.997 17180 Z= 0.303 Chirality : 0.042 0.154 1886 Planarity : 0.004 0.048 2080 Dihedral : 13.060 165.164 2006 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 2.25 % Allowed : 18.79 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.22), residues: 1445 helix: 1.02 (0.21), residues: 665 sheet: -0.33 (0.53), residues: 115 loop : -2.19 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 578 TYR 0.014 0.001 TYR C 104 PHE 0.021 0.001 PHE B 108 TRP 0.040 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00254 (12687) covalent geometry : angle 0.60882 (17180) hydrogen bonds : bond 0.03645 ( 515) hydrogen bonds : angle 4.03766 ( 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 262 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8268 (tmm) cc_final: 0.7565 (tmm) REVERT: A 222 GLN cc_start: 0.8162 (mm110) cc_final: 0.7821 (mm-40) REVERT: A 339 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (ptt180) REVERT: A 426 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 427 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8660 (tt) REVERT: A 587 LEU cc_start: 0.8611 (mm) cc_final: 0.8390 (mm) REVERT: A 622 ASP cc_start: 0.8047 (t70) cc_final: 0.7241 (t0) REVERT: A 702 LYS cc_start: 0.8133 (tmtt) cc_final: 0.7689 (ttpp) REVERT: B 41 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 71 THR cc_start: 0.8516 (p) cc_final: 0.8217 (p) REVERT: B 140 MET cc_start: 0.7355 (mtp) cc_final: 0.6982 (mtt) REVERT: B 148 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8764 (mp) REVERT: B 151 ASP cc_start: 0.7787 (t0) cc_final: 0.7495 (t0) REVERT: B 184 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6156 (pttt) REVERT: B 222 ARG cc_start: 0.8566 (ttm170) cc_final: 0.7683 (ttt180) REVERT: B 248 MET cc_start: 0.8028 (tpp) cc_final: 0.7590 (tpp) REVERT: B 266 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 388 ASP cc_start: 0.8130 (m-30) cc_final: 0.7657 (m-30) REVERT: B 578 ARG cc_start: 0.8604 (ttm110) cc_final: 0.8250 (mtp85) REVERT: B 710 MET cc_start: 0.7909 (mmt) cc_final: 0.7365 (tpt) REVERT: B 748 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7663 (mmm160) REVERT: C 38 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7643 (m100) REVERT: C 164 LYS cc_start: 0.8682 (tppt) cc_final: 0.7922 (tppt) REVERT: C 168 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 231 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8567 (mm) outliers start: 29 outliers final: 20 residues processed: 251 average time/residue: 0.1089 time to fit residues: 39.5138 Evaluate side-chains 252 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 336 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU 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 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 305 THR 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 C residue 34 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 231 ILE 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: 7.9990 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 138 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 134 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112754 restraints weight = 19331.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116307 restraints weight = 10039.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118694 restraints weight = 6590.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120197 restraints weight = 4989.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121072 restraints weight = 4186.216| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12687 Z= 0.111 Angle : 0.607 9.296 17180 Z= 0.303 Chirality : 0.041 0.151 1886 Planarity : 0.004 0.049 2080 Dihedral : 13.017 165.058 2006 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 1.94 % Allowed : 19.57 % Favored : 78.49 % 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: -0.70 (0.22), residues: 1445 helix: 1.04 (0.21), residues: 666 sheet: -0.29 (0.53), residues: 117 loop : -2.17 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.019 0.001 TYR C 11 PHE 0.021 0.001 PHE B 108 TRP 0.034 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00249 (12687) covalent geometry : angle 0.60749 (17180) hydrogen bonds : bond 0.03564 ( 515) hydrogen bonds : angle 3.98252 ( 1430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.17 seconds wall clock time: 35 minutes 51.36 seconds (2151.36 seconds total)