Starting phenix.real_space_refine on Wed Mar 4 14:32:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kut_9580/03_2026/6kut_9580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kut_9580/03_2026/6kut_9580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kut_9580/03_2026/6kut_9580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kut_9580/03_2026/6kut_9580_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kut_9580/03_2026/6kut_9580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kut_9580/03_2026/6kut_9580.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 27 5.49 5 S 116 5.16 5 C 8862 2.51 5 N 2411 2.21 5 O 2695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s 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: 14111 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5639 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 663} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5533 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 669} Chain breaks: 5 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: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2360 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, '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: 3.54, per 1000 atoms: 0.25 Number of scatterers: 14111 At special positions: 0 Unit cell: (115.6, 110.16, 126.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 27 15.00 O 2695 8.00 N 2411 7.00 C 8862 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: 1.29 Conformation dependent library (CDL) restraints added in 497.9 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 15 sheets defined 45.9% alpha, 7.7% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.520A pdb=" N ILE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.919A pdb=" N SER A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.168A pdb=" N THR A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.701A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.501A pdb=" N ALA A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.870A 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: 3.663A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 569 through 589 removed outlier: 3.811A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.657A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 684 through 703 removed outlier: 3.607A pdb=" N SER A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 4.011A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.557A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.994A 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 116 removed outlier: 3.618A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 removed outlier: 3.558A pdb=" N GLN B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.637A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.518A 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 293 removed outlier: 3.579A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.845A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.646A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.618A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.800A 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: 3.868A 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: 3.596A 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 513 removed outlier: 3.789A pdb=" N ALA B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.512A pdb=" N ALA B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.617A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.900A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.570A pdb=" N GLY B 595 " --> pdb=" O ILE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.783A 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 removed outlier: 3.502A pdb=" N PHE B 626 " --> pdb=" O ARG B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 removed outlier: 3.611A pdb=" N LYS B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 4.473A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.646A pdb=" N TYR B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 752 " --> pdb=" O ARG B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.660A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.529A pdb=" N ILE C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.927A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 218 removed outlier: 3.806A pdb=" N PHE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.892A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 727 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 109 removed outlier: 5.854A pdb=" N GLU A 105 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 133 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY A 107 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.382A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.575A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.734A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.622A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AB6, first strand: chain 'C' and resid 736 through 740 566 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4212 1.34 - 1.46: 2632 1.46 - 1.58: 7354 1.58 - 1.70: 52 1.70 - 1.82: 191 Bond restraints: 14441 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.27e-02 6.20e+03 9.97e+00 bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C ILE C 73 " pdb=" N PRO C 74 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.30e-02 5.92e+03 3.85e+00 bond pdb=" C LEU B 487 " pdb=" N PRO B 488 " ideal model delta sigma weight residual 1.334 1.378 -0.045 2.34e-02 1.83e+03 3.62e+00 bond pdb=" O5' C R 4 " pdb=" C5' C R 4 " ideal model delta sigma weight residual 1.420 1.444 -0.024 1.50e-02 4.44e+03 2.62e+00 ... (remaining 14436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 19141 2.40 - 4.80: 330 4.80 - 7.20: 46 7.20 - 9.60: 13 9.60 - 12.00: 3 Bond angle restraints: 19533 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 109.40 121.40 -12.00 1.50e+00 4.44e-01 6.40e+01 angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.53 107.10 6.43 9.80e-01 1.04e+00 4.30e+01 angle pdb=" CA ILE C 186 " pdb=" CB ILE C 186 " pdb=" CG2 ILE C 186 " ideal model delta sigma weight residual 110.50 117.45 -6.95 1.70e+00 3.46e-01 1.67e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 122.18 -8.08 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N ASP C 716 " pdb=" CA ASP C 716 " pdb=" C ASP C 716 " ideal model delta sigma weight residual 112.35 117.63 -5.28 1.34e+00 5.57e-01 1.55e+01 ... (remaining 19528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 8763 35.93 - 71.87: 105 71.87 - 107.80: 10 107.80 - 143.73: 1 143.73 - 179.66: 1 Dihedral angle restraints: 8880 sinusoidal: 3986 harmonic: 4894 Sorted by residual: dihedral pdb=" CA LEU C 181 " pdb=" C LEU C 181 " pdb=" N ALA C 182 " pdb=" CA ALA C 182 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL C 740 " pdb=" C VAL C 740 " pdb=" N GLY C 741 " pdb=" CA GLY C 741 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE B 726 " pdb=" C PHE B 726 " pdb=" N GLU B 727 " pdb=" CA GLU B 727 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2084 0.121 - 0.242: 51 0.242 - 0.362: 5 0.362 - 0.483: 1 0.483 - 0.604: 1 Chirality restraints: 2142 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 -2.14 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CB ILE C 186 " pdb=" CA ILE C 186 " pdb=" CG1 ILE C 186 " pdb=" CG2 ILE C 186 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.68e+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 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2139 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 36 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ILE A 36 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 37 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 35 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C MET A 35 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 35 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 37 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C SER A 37 " 0.048 2.00e-02 2.50e+03 pdb=" O SER A 37 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 38 " -0.016 2.00e-02 2.50e+03 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 841 2.73 - 3.27: 13142 3.27 - 3.82: 21297 3.82 - 4.36: 26311 4.36 - 4.90: 44451 Nonbonded interactions: 106042 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.191 3.120 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.248 3.120 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 163 " pdb=" NH1 ARG A 167 " model vdw 2.282 3.120 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.291 3.040 ... (remaining 106037 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: 0.530 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.260 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14441 Z= 0.177 Angle : 0.807 11.996 19533 Z= 0.445 Chirality : 0.053 0.604 2142 Planarity : 0.006 0.056 2391 Dihedral : 11.953 179.664 5704 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 0.68 % Allowed : 2.17 % Favored : 97.16 % 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: -5.00 (0.15), residues: 1653 helix: -3.60 (0.11), residues: 711 sheet: -1.73 (0.42), residues: 143 loop : -3.35 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 438 TYR 0.018 0.002 TYR B 22 PHE 0.023 0.002 PHE A 156 TRP 0.030 0.002 TRP A 386 HIS 0.010 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00345 (14441) covalent geometry : angle 0.80665 (19533) hydrogen bonds : bond 0.14163 ( 583) hydrogen bonds : angle 9.82739 ( 1618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 559 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7328 (ttp80) cc_final: 0.7001 (ptp90) REVERT: A 68 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.3899 (tt) REVERT: A 171 MET cc_start: 0.6165 (mtm) cc_final: 0.5770 (mtt) REVERT: A 340 ASP cc_start: 0.8500 (m-30) cc_final: 0.8151 (m-30) REVERT: A 350 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7731 (ttpp) REVERT: A 365 PHE cc_start: 0.6679 (t80) cc_final: 0.6117 (t80) REVERT: A 427 LEU cc_start: 0.9231 (tt) cc_final: 0.8605 (tt) REVERT: A 497 MET cc_start: 0.8129 (mpt) cc_final: 0.7253 (mmt) REVERT: A 511 ASN cc_start: 0.8176 (t0) cc_final: 0.7933 (t0) REVERT: A 526 VAL cc_start: 0.9302 (t) cc_final: 0.8995 (p) REVERT: A 561 ASP cc_start: 0.7017 (t70) cc_final: 0.6717 (t70) REVERT: A 565 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8473 (mtmm) REVERT: A 619 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8039 (tmtt) REVERT: A 649 GLN cc_start: 0.8429 (pt0) cc_final: 0.8171 (pt0) REVERT: B 335 MET cc_start: 0.7270 (ttt) cc_final: 0.6958 (tpp) REVERT: B 336 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7602 (ttmm) REVERT: B 341 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7488 (p) REVERT: B 393 ILE cc_start: 0.9419 (tt) cc_final: 0.8046 (tt) REVERT: B 415 MET cc_start: 0.6892 (mtt) cc_final: 0.6643 (mtt) REVERT: B 490 LEU cc_start: 0.8837 (tp) cc_final: 0.8388 (tp) REVERT: B 574 MET cc_start: 0.6910 (mmm) cc_final: 0.6654 (tpt) REVERT: B 678 MET cc_start: 0.2875 (mmt) cc_final: 0.2091 (tpp) REVERT: B 685 TYR cc_start: 0.6774 (m-10) cc_final: 0.6495 (m-80) REVERT: B 715 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8313 (pp20) REVERT: C 9 LYS cc_start: 0.7809 (tttm) cc_final: 0.7215 (mttm) REVERT: C 13 ASN cc_start: 0.7450 (m-40) cc_final: 0.7084 (m-40) REVERT: C 69 GLU cc_start: 0.7184 (pt0) cc_final: 0.6854 (pp20) REVERT: C 81 ASP cc_start: 0.7285 (m-30) cc_final: 0.7040 (m-30) REVERT: C 190 PHE cc_start: 0.6241 (t80) cc_final: 0.5978 (t80) outliers start: 10 outliers final: 0 residues processed: 565 average time/residue: 0.1409 time to fit residues: 111.8400 Evaluate side-chains 326 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN A 170 ASN A 263 HIS A 638 ASN A 670 GLN B 70 ASN B 147 GLN B 154 GLN B 170 ASN B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 572 HIS ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN C 742 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.159328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127092 restraints weight = 25153.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130367 restraints weight = 14291.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132494 restraints weight = 9521.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133855 restraints weight = 7190.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134648 restraints weight = 5965.309| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14441 Z= 0.156 Angle : 0.646 8.534 19533 Z= 0.340 Chirality : 0.043 0.229 2142 Planarity : 0.005 0.064 2391 Dihedral : 12.649 164.525 2227 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.18), residues: 1653 helix: -1.32 (0.17), residues: 733 sheet: -1.12 (0.47), residues: 130 loop : -3.11 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 330 TYR 0.014 0.001 TYR B 47 PHE 0.028 0.001 PHE A 161 TRP 0.015 0.001 TRP A 386 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00343 (14441) covalent geometry : angle 0.64613 (19533) hydrogen bonds : bond 0.04803 ( 583) hydrogen bonds : angle 5.78385 ( 1618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7216 (ptp90) REVERT: A 207 ASN cc_start: 0.8167 (m-40) cc_final: 0.7880 (m-40) REVERT: A 365 PHE cc_start: 0.6768 (t80) cc_final: 0.6240 (t80) REVERT: A 427 LEU cc_start: 0.9236 (tt) cc_final: 0.8709 (tt) REVERT: A 439 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8028 (tp30) REVERT: A 442 LYS cc_start: 0.9186 (tttt) cc_final: 0.8735 (ttmm) REVERT: A 497 MET cc_start: 0.8440 (mpp) cc_final: 0.8017 (mmt) REVERT: A 511 ASN cc_start: 0.8615 (t0) cc_final: 0.8277 (t0) REVERT: A 516 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 561 ASP cc_start: 0.8180 (t70) cc_final: 0.7806 (t70) REVERT: A 619 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7358 (tmtt) REVERT: B 17 MET cc_start: 0.8660 (mmm) cc_final: 0.8455 (mmm) REVERT: B 93 LEU cc_start: 0.8963 (mt) cc_final: 0.8541 (mp) REVERT: B 96 MET cc_start: 0.8408 (mtt) cc_final: 0.7997 (mtt) REVERT: B 116 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7414 (mp0) REVERT: B 130 GLN cc_start: 0.8240 (tp40) cc_final: 0.7503 (tp40) REVERT: B 254 SER cc_start: 0.9063 (p) cc_final: 0.8532 (t) REVERT: B 289 SER cc_start: 0.8967 (m) cc_final: 0.8679 (p) REVERT: B 301 MET cc_start: 0.8362 (ttm) cc_final: 0.8071 (ttm) REVERT: B 311 TRP cc_start: 0.8743 (t-100) cc_final: 0.8512 (t-100) REVERT: B 336 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8105 (ttmm) REVERT: B 341 VAL cc_start: 0.8164 (p) cc_final: 0.7782 (p) REVERT: B 382 MET cc_start: 0.7922 (mtp) cc_final: 0.7612 (mmm) REVERT: B 383 ASN cc_start: 0.8056 (m110) cc_final: 0.7366 (m110) REVERT: B 413 PHE cc_start: 0.7513 (m-10) cc_final: 0.7297 (m-10) REVERT: B 423 MET cc_start: 0.8877 (mtm) cc_final: 0.8615 (mtm) REVERT: B 490 LEU cc_start: 0.8786 (tp) cc_final: 0.8241 (tp) REVERT: B 547 MET cc_start: 0.8411 (ttm) cc_final: 0.8147 (ttt) REVERT: B 574 MET cc_start: 0.7832 (mmm) cc_final: 0.7596 (tpt) REVERT: B 624 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7086 (ttt180) REVERT: B 678 MET cc_start: 0.2863 (mmt) cc_final: 0.1331 (ttt) REVERT: B 715 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8646 (mt-10) REVERT: C 17 ASP cc_start: 0.7797 (t0) cc_final: 0.7418 (t0) REVERT: C 69 GLU cc_start: 0.7665 (pt0) cc_final: 0.7456 (pp20) REVERT: C 70 GLU cc_start: 0.7939 (pp20) cc_final: 0.7640 (pp20) REVERT: C 140 MET cc_start: 0.8516 (mtp) cc_final: 0.8150 (mtm) REVERT: C 246 PHE cc_start: 0.9161 (m-10) cc_final: 0.8864 (m-10) REVERT: C 247 TRP cc_start: 0.9133 (p-90) cc_final: 0.8707 (p-90) REVERT: C 249 ILE cc_start: 0.8529 (tt) cc_final: 0.8265 (pt) outliers start: 1 outliers final: 0 residues processed: 403 average time/residue: 0.1293 time to fit residues: 74.4338 Evaluate side-chains 316 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 170 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS C 216 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126807 restraints weight = 25635.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130049 restraints weight = 14563.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132203 restraints weight = 9787.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133548 restraints weight = 7434.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134468 restraints weight = 6168.520| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14441 Z= 0.127 Angle : 0.599 7.779 19533 Z= 0.312 Chirality : 0.042 0.241 2142 Planarity : 0.004 0.057 2391 Dihedral : 12.442 165.441 2227 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.62 % Rotamer: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % 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: -2.32 (0.19), residues: 1653 helix: -0.41 (0.18), residues: 737 sheet: -0.90 (0.48), residues: 129 loop : -2.85 (0.19), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 330 TYR 0.012 0.001 TYR A 708 PHE 0.046 0.001 PHE A 161 TRP 0.017 0.001 TRP A 386 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00273 (14441) covalent geometry : angle 0.59948 (19533) hydrogen bonds : bond 0.04232 ( 583) hydrogen bonds : angle 5.19638 ( 1618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7141 (ptp90) REVERT: A 34 THR cc_start: 0.8667 (p) cc_final: 0.8176 (t) REVERT: A 47 LEU cc_start: 0.8155 (mt) cc_final: 0.7939 (tp) REVERT: A 235 ARG cc_start: 0.6348 (tpm170) cc_final: 0.5846 (tpp-160) REVERT: A 327 LYS cc_start: 0.8887 (tttm) cc_final: 0.8555 (mmmt) REVERT: A 365 PHE cc_start: 0.6788 (t80) cc_final: 0.6394 (t80) REVERT: A 427 LEU cc_start: 0.9030 (tt) cc_final: 0.8558 (tt) REVERT: A 428 GLU cc_start: 0.8165 (tp30) cc_final: 0.7838 (tp30) REVERT: A 439 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8097 (tp30) REVERT: A 497 MET cc_start: 0.8457 (mpp) cc_final: 0.7925 (mmt) REVERT: A 511 ASN cc_start: 0.8692 (t0) cc_final: 0.8366 (t0) REVERT: A 516 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 561 ASP cc_start: 0.8182 (t70) cc_final: 0.7843 (t70) REVERT: A 603 TRP cc_start: 0.7057 (m-90) cc_final: 0.6693 (m-90) REVERT: A 619 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8003 (mmtp) REVERT: A 649 GLN cc_start: 0.8668 (pt0) cc_final: 0.8448 (pt0) REVERT: A 650 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8237 (mtmm) REVERT: B 1 MET cc_start: 0.6709 (ttp) cc_final: 0.5750 (tmm) REVERT: B 17 MET cc_start: 0.8708 (mmm) cc_final: 0.8437 (mmm) REVERT: B 116 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7301 (mp0) REVERT: B 130 GLN cc_start: 0.8225 (tp40) cc_final: 0.7943 (tp40) REVERT: B 254 SER cc_start: 0.9113 (p) cc_final: 0.8731 (t) REVERT: B 289 SER cc_start: 0.8926 (m) cc_final: 0.8597 (p) REVERT: B 335 MET cc_start: 0.7750 (tpp) cc_final: 0.7466 (tpp) REVERT: B 336 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8220 (ttmm) REVERT: B 341 VAL cc_start: 0.7911 (p) cc_final: 0.7447 (p) REVERT: B 382 MET cc_start: 0.7906 (mtp) cc_final: 0.7662 (mmm) REVERT: B 423 MET cc_start: 0.8811 (mtm) cc_final: 0.8556 (mtm) REVERT: B 479 SER cc_start: 0.8712 (t) cc_final: 0.8441 (t) REVERT: B 490 LEU cc_start: 0.8819 (tp) cc_final: 0.8276 (tp) REVERT: B 519 ASN cc_start: 0.8599 (t0) cc_final: 0.8077 (t0) REVERT: B 522 THR cc_start: 0.8808 (p) cc_final: 0.8493 (t) REVERT: B 547 MET cc_start: 0.8549 (ttm) cc_final: 0.8218 (ttt) REVERT: B 574 MET cc_start: 0.7930 (mmm) cc_final: 0.7681 (tpt) REVERT: B 602 ILE cc_start: 0.9145 (tt) cc_final: 0.8929 (tt) REVERT: B 624 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7046 (ttt180) REVERT: C 6 THR cc_start: 0.7642 (p) cc_final: 0.7123 (p) REVERT: C 62 MET cc_start: 0.7990 (ttm) cc_final: 0.7561 (ttp) REVERT: C 70 GLU cc_start: 0.8101 (pp20) cc_final: 0.7875 (pp20) REVERT: C 247 TRP cc_start: 0.9144 (p-90) cc_final: 0.8777 (p-90) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.1272 time to fit residues: 70.9821 Evaluate side-chains 299 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 67 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN B 170 ASN B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122143 restraints weight = 25850.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125255 restraints weight = 14938.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127287 restraints weight = 10164.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128538 restraints weight = 7778.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129426 restraints weight = 6541.187| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14441 Z= 0.175 Angle : 0.638 7.741 19533 Z= 0.333 Chirality : 0.044 0.235 2142 Planarity : 0.004 0.056 2391 Dihedral : 12.425 164.673 2227 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % 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: -1.94 (0.20), residues: 1653 helix: -0.01 (0.19), residues: 736 sheet: -0.85 (0.51), residues: 119 loop : -2.70 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 724 TYR 0.013 0.002 TYR C 11 PHE 0.021 0.002 PHE A 156 TRP 0.016 0.001 TRP A 386 HIS 0.008 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00396 (14441) covalent geometry : angle 0.63762 (19533) hydrogen bonds : bond 0.04506 ( 583) hydrogen bonds : angle 5.00448 ( 1618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7084 (ptp90) REVERT: A 34 THR cc_start: 0.8687 (p) cc_final: 0.8070 (t) REVERT: A 47 LEU cc_start: 0.8318 (mt) cc_final: 0.8074 (tp) REVERT: A 365 PHE cc_start: 0.6977 (t80) cc_final: 0.6599 (t80) REVERT: A 428 GLU cc_start: 0.8127 (tp30) cc_final: 0.7807 (tp30) REVERT: A 497 MET cc_start: 0.8430 (mpp) cc_final: 0.7850 (mmt) REVERT: A 511 ASN cc_start: 0.8814 (t0) cc_final: 0.8444 (t0) REVERT: A 516 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 565 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8444 (mtmm) REVERT: A 619 LYS cc_start: 0.8491 (mmtt) cc_final: 0.7987 (mmtp) REVERT: A 649 GLN cc_start: 0.8678 (pt0) cc_final: 0.8372 (pt0) REVERT: B 61 PHE cc_start: 0.8717 (m-80) cc_final: 0.8463 (m-80) REVERT: B 116 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7226 (mp0) REVERT: B 123 SER cc_start: 0.8067 (p) cc_final: 0.7822 (p) REVERT: B 130 GLN cc_start: 0.8219 (tp40) cc_final: 0.7493 (tp40) REVERT: B 254 SER cc_start: 0.9037 (p) cc_final: 0.8562 (t) REVERT: B 289 SER cc_start: 0.9021 (m) cc_final: 0.8760 (p) REVERT: B 336 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8128 (ttmm) REVERT: B 341 VAL cc_start: 0.7898 (p) cc_final: 0.7591 (p) REVERT: B 382 MET cc_start: 0.8038 (mtp) cc_final: 0.7817 (mmm) REVERT: B 413 PHE cc_start: 0.7712 (m-10) cc_final: 0.7426 (m-80) REVERT: B 415 MET cc_start: 0.7478 (mtt) cc_final: 0.7234 (mtt) REVERT: B 423 MET cc_start: 0.8881 (mtm) cc_final: 0.8638 (mtm) REVERT: B 442 LEU cc_start: 0.8661 (tp) cc_final: 0.8330 (mp) REVERT: B 490 LEU cc_start: 0.8838 (tp) cc_final: 0.8417 (tp) REVERT: B 519 ASN cc_start: 0.8522 (t0) cc_final: 0.8237 (t0) REVERT: B 520 GLU cc_start: 0.8209 (tt0) cc_final: 0.7883 (tt0) REVERT: B 522 THR cc_start: 0.8788 (p) cc_final: 0.8486 (t) REVERT: B 624 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7363 (ttt180) REVERT: B 678 MET cc_start: 0.2775 (mmt) cc_final: 0.1029 (ttt) REVERT: C 62 MET cc_start: 0.8122 (ttm) cc_final: 0.7807 (ttp) REVERT: C 140 MET cc_start: 0.8582 (mtp) cc_final: 0.8353 (mtm) REVERT: C 247 TRP cc_start: 0.9147 (p-90) cc_final: 0.8853 (p-90) outliers start: 1 outliers final: 1 residues processed: 361 average time/residue: 0.1244 time to fit residues: 65.0504 Evaluate side-chains 293 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 129 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 115 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123198 restraints weight = 25319.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126271 restraints weight = 14298.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128266 restraints weight = 9555.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129557 restraints weight = 7261.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130466 restraints weight = 6029.087| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14441 Z= 0.119 Angle : 0.598 8.116 19533 Z= 0.309 Chirality : 0.042 0.265 2142 Planarity : 0.004 0.055 2391 Dihedral : 12.346 164.035 2227 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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 (0.20), residues: 1653 helix: 0.38 (0.19), residues: 735 sheet: -0.67 (0.50), residues: 120 loop : -2.58 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 129 TYR 0.012 0.001 TYR A 708 PHE 0.021 0.001 PHE C 224 TRP 0.010 0.001 TRP A 386 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00265 (14441) covalent geometry : angle 0.59804 (19533) hydrogen bonds : bond 0.03903 ( 583) hydrogen bonds : angle 4.69418 ( 1618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7055 (ptp90) REVERT: A 34 THR cc_start: 0.8708 (p) cc_final: 0.8161 (t) REVERT: A 47 LEU cc_start: 0.8298 (mt) cc_final: 0.8095 (tp) REVERT: A 327 LYS cc_start: 0.8872 (tttm) cc_final: 0.8650 (mmmt) REVERT: A 365 PHE cc_start: 0.6978 (t80) cc_final: 0.6673 (t80) REVERT: A 428 GLU cc_start: 0.8120 (tp30) cc_final: 0.7915 (tp30) REVERT: A 497 MET cc_start: 0.8312 (mpp) cc_final: 0.7700 (mmt) REVERT: A 511 ASN cc_start: 0.8832 (t0) cc_final: 0.8397 (t0) REVERT: A 514 LYS cc_start: 0.9068 (tttt) cc_final: 0.8408 (tttp) REVERT: A 516 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 561 ASP cc_start: 0.8377 (t70) cc_final: 0.7989 (t70) REVERT: A 565 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8675 (mttm) REVERT: A 619 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7913 (mmtp) REVERT: A 650 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7685 (mtmm) REVERT: B 89 PHE cc_start: 0.9130 (t80) cc_final: 0.8638 (t80) REVERT: B 116 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7015 (mp0) REVERT: B 123 SER cc_start: 0.8241 (p) cc_final: 0.7951 (p) REVERT: B 130 GLN cc_start: 0.8225 (tp40) cc_final: 0.7460 (tp40) REVERT: B 254 SER cc_start: 0.9000 (p) cc_final: 0.8542 (t) REVERT: B 289 SER cc_start: 0.8978 (m) cc_final: 0.8639 (p) REVERT: B 336 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8173 (ttmm) REVERT: B 341 VAL cc_start: 0.7920 (p) cc_final: 0.7623 (p) REVERT: B 381 LEU cc_start: 0.8482 (mp) cc_final: 0.8259 (mp) REVERT: B 413 PHE cc_start: 0.7616 (m-10) cc_final: 0.7411 (m-80) REVERT: B 415 MET cc_start: 0.7404 (mtt) cc_final: 0.7176 (mtt) REVERT: B 423 MET cc_start: 0.8771 (mtm) cc_final: 0.8567 (mtm) REVERT: B 442 LEU cc_start: 0.8568 (tp) cc_final: 0.8316 (mp) REVERT: B 490 LEU cc_start: 0.8851 (tp) cc_final: 0.8446 (tp) REVERT: B 522 THR cc_start: 0.8828 (p) cc_final: 0.8517 (t) REVERT: B 547 MET cc_start: 0.8337 (ttm) cc_final: 0.7996 (ttt) REVERT: B 663 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7627 (ttt180) REVERT: B 678 MET cc_start: 0.2718 (mmt) cc_final: 0.0977 (ttt) REVERT: C 62 MET cc_start: 0.8228 (ttm) cc_final: 0.7901 (ttp) REVERT: C 140 MET cc_start: 0.8538 (mtp) cc_final: 0.8284 (mtp) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1199 time to fit residues: 63.1511 Evaluate side-chains 289 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 170 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.153573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120936 restraints weight = 25822.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123910 restraints weight = 14978.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125881 restraints weight = 10277.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127171 restraints weight = 7928.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127911 restraints weight = 6655.974| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14441 Z= 0.167 Angle : 0.643 7.656 19533 Z= 0.333 Chirality : 0.044 0.229 2142 Planarity : 0.004 0.055 2391 Dihedral : 12.376 164.542 2227 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.56 % Rotamer: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % 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: -1.49 (0.20), residues: 1653 helix: 0.40 (0.19), residues: 740 sheet: -0.61 (0.50), residues: 121 loop : -2.51 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 567 TYR 0.013 0.002 TYR A 708 PHE 0.018 0.002 PHE B 122 TRP 0.034 0.002 TRP A 357 HIS 0.008 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00382 (14441) covalent geometry : angle 0.64304 (19533) hydrogen bonds : bond 0.04320 ( 583) hydrogen bonds : angle 4.77380 ( 1618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8772 (p) cc_final: 0.8205 (t) REVERT: A 43 GLN cc_start: 0.8539 (tp40) cc_final: 0.8281 (tp40) REVERT: A 171 MET cc_start: 0.5647 (mtt) cc_final: 0.5436 (mtp) REVERT: A 297 MET cc_start: 0.6938 (mmt) cc_final: 0.6412 (mmt) REVERT: A 327 LYS cc_start: 0.8917 (tttm) cc_final: 0.8684 (mmmt) REVERT: A 350 LYS cc_start: 0.8583 (tttt) cc_final: 0.8269 (ttpp) REVERT: A 357 TRP cc_start: 0.5818 (t60) cc_final: 0.5547 (t60) REVERT: A 365 PHE cc_start: 0.7054 (t80) cc_final: 0.6769 (t80) REVERT: A 428 GLU cc_start: 0.8224 (tp30) cc_final: 0.7904 (tp30) REVERT: A 497 MET cc_start: 0.8365 (mpp) cc_final: 0.7774 (mmt) REVERT: A 511 ASN cc_start: 0.8875 (t0) cc_final: 0.8469 (t0) REVERT: A 516 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 565 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8759 (mttm) REVERT: A 574 MET cc_start: 0.8454 (mmm) cc_final: 0.8240 (mmm) REVERT: A 619 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8077 (mmtp) REVERT: B 123 SER cc_start: 0.8144 (p) cc_final: 0.7903 (p) REVERT: B 130 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7899 (tp-100) REVERT: B 254 SER cc_start: 0.9134 (p) cc_final: 0.8648 (t) REVERT: B 289 SER cc_start: 0.9012 (m) cc_final: 0.8703 (p) REVERT: B 336 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8034 (ttmm) REVERT: B 341 VAL cc_start: 0.7940 (p) cc_final: 0.7586 (p) REVERT: B 381 LEU cc_start: 0.8233 (mp) cc_final: 0.7962 (mp) REVERT: B 413 PHE cc_start: 0.7714 (m-10) cc_final: 0.7450 (m-80) REVERT: B 415 MET cc_start: 0.7465 (mtt) cc_final: 0.7252 (mtt) REVERT: B 423 MET cc_start: 0.8924 (mtm) cc_final: 0.8706 (mtm) REVERT: B 442 LEU cc_start: 0.8632 (tp) cc_final: 0.8287 (mp) REVERT: B 490 LEU cc_start: 0.8903 (tp) cc_final: 0.8510 (tp) REVERT: B 522 THR cc_start: 0.8906 (p) cc_final: 0.8581 (t) REVERT: B 547 MET cc_start: 0.8312 (ttm) cc_final: 0.8083 (ttp) REVERT: B 571 ASN cc_start: 0.8319 (p0) cc_final: 0.8059 (p0) REVERT: B 574 MET cc_start: 0.7908 (mmm) cc_final: 0.7278 (tpt) REVERT: B 663 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7771 (ttt180) REVERT: B 678 MET cc_start: 0.2315 (mmt) cc_final: 0.0722 (ttt) REVERT: B 692 TYR cc_start: 0.7483 (t80) cc_final: 0.7134 (t80) REVERT: B 717 LYS cc_start: 0.8505 (tppt) cc_final: 0.8175 (tppt) REVERT: C 62 MET cc_start: 0.8279 (ttm) cc_final: 0.7951 (ttp) REVERT: C 140 MET cc_start: 0.8571 (mtp) cc_final: 0.8309 (mtm) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1202 time to fit residues: 58.9456 Evaluate side-chains 283 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 0.0020 chunk 146 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 160 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 277 HIS ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124961 restraints weight = 25562.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128068 restraints weight = 14619.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130074 restraints weight = 9891.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131481 restraints weight = 7568.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132300 restraints weight = 6295.685| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14441 Z= 0.111 Angle : 0.596 7.421 19533 Z= 0.306 Chirality : 0.042 0.220 2142 Planarity : 0.004 0.055 2391 Dihedral : 12.304 164.039 2227 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.11 % 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: -1.22 (0.21), residues: 1653 helix: 0.66 (0.19), residues: 731 sheet: -0.48 (0.51), residues: 120 loop : -2.37 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.013 0.001 TYR A 708 PHE 0.019 0.001 PHE B 726 TRP 0.024 0.001 TRP A 357 HIS 0.011 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00242 (14441) covalent geometry : angle 0.59586 (19533) hydrogen bonds : bond 0.03724 ( 583) hydrogen bonds : angle 4.53473 ( 1618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7585 (ttp80) cc_final: 0.6766 (ptp90) REVERT: A 34 THR cc_start: 0.8649 (p) cc_final: 0.8073 (t) REVERT: A 43 GLN cc_start: 0.8437 (tp40) cc_final: 0.8207 (tp40) REVERT: A 350 LYS cc_start: 0.8618 (tttt) cc_final: 0.8359 (ttpp) REVERT: A 357 TRP cc_start: 0.5809 (t60) cc_final: 0.5566 (t60) REVERT: A 365 PHE cc_start: 0.6899 (t80) cc_final: 0.6698 (t80) REVERT: A 428 GLU cc_start: 0.8237 (tp30) cc_final: 0.7947 (tp30) REVERT: A 497 MET cc_start: 0.8305 (mpp) cc_final: 0.7712 (mmt) REVERT: A 511 ASN cc_start: 0.8829 (t0) cc_final: 0.8411 (t0) REVERT: A 514 LYS cc_start: 0.9088 (tttt) cc_final: 0.8624 (tttm) REVERT: A 516 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 561 ASP cc_start: 0.8460 (t70) cc_final: 0.8089 (t70) REVERT: A 565 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8714 (mttm) REVERT: A 574 MET cc_start: 0.8257 (mmm) cc_final: 0.7997 (mmm) REVERT: A 619 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8090 (mmtp) REVERT: A 650 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8085 (mtmm) REVERT: B 79 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 89 PHE cc_start: 0.9110 (t80) cc_final: 0.8613 (t80) REVERT: B 93 LEU cc_start: 0.8647 (mp) cc_final: 0.8342 (mp) REVERT: B 96 MET cc_start: 0.7871 (mpp) cc_final: 0.7209 (mtt) REVERT: B 130 GLN cc_start: 0.8473 (tp-100) cc_final: 0.7792 (tp-100) REVERT: B 220 ILE cc_start: 0.9320 (mm) cc_final: 0.9038 (tp) REVERT: B 254 SER cc_start: 0.9016 (p) cc_final: 0.8524 (t) REVERT: B 289 SER cc_start: 0.8952 (m) cc_final: 0.8602 (p) REVERT: B 335 MET cc_start: 0.7287 (tpp) cc_final: 0.7018 (tpp) REVERT: B 336 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7978 (mtpp) REVERT: B 341 VAL cc_start: 0.7866 (p) cc_final: 0.7562 (p) REVERT: B 415 MET cc_start: 0.7382 (mtt) cc_final: 0.7142 (mtt) REVERT: B 423 MET cc_start: 0.8878 (mtm) cc_final: 0.8542 (mtm) REVERT: B 428 ARG cc_start: 0.7506 (mmp-170) cc_final: 0.6355 (mmt90) REVERT: B 442 LEU cc_start: 0.8588 (tp) cc_final: 0.8313 (mp) REVERT: B 490 LEU cc_start: 0.8842 (tp) cc_final: 0.8476 (tp) REVERT: B 514 THR cc_start: 0.8869 (p) cc_final: 0.8590 (t) REVERT: B 522 THR cc_start: 0.8913 (p) cc_final: 0.8457 (t) REVERT: B 547 MET cc_start: 0.8352 (ttm) cc_final: 0.7962 (ttm) REVERT: B 571 ASN cc_start: 0.8214 (p0) cc_final: 0.7989 (p0) REVERT: B 574 MET cc_start: 0.7863 (mmm) cc_final: 0.7222 (tpt) REVERT: B 678 MET cc_start: 0.2152 (mmt) cc_final: 0.0414 (ttt) REVERT: B 692 TYR cc_start: 0.7551 (t80) cc_final: 0.7040 (t80) REVERT: C 140 MET cc_start: 0.8519 (mtp) cc_final: 0.8195 (mtm) outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.1156 time to fit residues: 58.9159 Evaluate side-chains 282 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 87 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 63 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 152 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 170 ASN A 285 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124729 restraints weight = 25574.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127792 restraints weight = 14828.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129829 restraints weight = 10108.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131187 restraints weight = 7754.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131916 restraints weight = 6476.518| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14441 Z= 0.122 Angle : 0.626 8.381 19533 Z= 0.320 Chirality : 0.043 0.249 2142 Planarity : 0.004 0.056 2391 Dihedral : 12.262 164.108 2227 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.14 % Allowed : 0.88 % Favored : 98.99 % 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: -1.23 (0.20), residues: 1653 helix: 0.59 (0.19), residues: 737 sheet: -0.46 (0.51), residues: 121 loop : -2.33 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 724 TYR 0.013 0.001 TYR A 52 PHE 0.015 0.001 PHE B 420 TRP 0.022 0.001 TRP A 357 HIS 0.009 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00272 (14441) covalent geometry : angle 0.62580 (19533) hydrogen bonds : bond 0.03778 ( 583) hydrogen bonds : angle 4.53961 ( 1618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7589 (ttp80) cc_final: 0.6642 (ptp90) REVERT: A 34 THR cc_start: 0.8703 (p) cc_final: 0.8108 (t) REVERT: A 43 GLN cc_start: 0.8432 (tp40) cc_final: 0.8198 (tp40) REVERT: A 350 LYS cc_start: 0.8526 (tttt) cc_final: 0.8261 (ttpp) REVERT: A 365 PHE cc_start: 0.6984 (t80) cc_final: 0.6763 (t80) REVERT: A 428 GLU cc_start: 0.8243 (tp30) cc_final: 0.7985 (tp30) REVERT: A 497 MET cc_start: 0.8263 (mpp) cc_final: 0.7614 (mmt) REVERT: A 511 ASN cc_start: 0.8849 (t0) cc_final: 0.8444 (t0) REVERT: A 514 LYS cc_start: 0.9130 (tttt) cc_final: 0.8653 (tttm) REVERT: A 516 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 561 ASP cc_start: 0.8404 (t70) cc_final: 0.8024 (t70) REVERT: A 565 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8730 (mttm) REVERT: A 574 MET cc_start: 0.8323 (mmm) cc_final: 0.7968 (mmm) REVERT: A 619 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8132 (mmtp) REVERT: B 79 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 130 GLN cc_start: 0.8537 (tp-100) cc_final: 0.7796 (tp-100) REVERT: B 176 MET cc_start: 0.8524 (mtp) cc_final: 0.8307 (mtm) REVERT: B 220 ILE cc_start: 0.9315 (mm) cc_final: 0.9074 (tp) REVERT: B 254 SER cc_start: 0.9239 (p) cc_final: 0.8701 (t) REVERT: B 289 SER cc_start: 0.8928 (m) cc_final: 0.8595 (p) REVERT: B 336 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8023 (ttmm) REVERT: B 341 VAL cc_start: 0.7766 (p) cc_final: 0.7447 (p) REVERT: B 415 MET cc_start: 0.7387 (mtt) cc_final: 0.7122 (mtt) REVERT: B 428 ARG cc_start: 0.7517 (mmp-170) cc_final: 0.6414 (mmt90) REVERT: B 442 LEU cc_start: 0.8618 (tp) cc_final: 0.8369 (mp) REVERT: B 490 LEU cc_start: 0.8889 (tp) cc_final: 0.8477 (tp) REVERT: B 522 THR cc_start: 0.9161 (p) cc_final: 0.8750 (t) REVERT: B 535 MET cc_start: 0.8246 (ttm) cc_final: 0.7814 (mtt) REVERT: B 547 MET cc_start: 0.8620 (ttm) cc_final: 0.8160 (ttt) REVERT: B 571 ASN cc_start: 0.8133 (p0) cc_final: 0.7847 (p0) REVERT: B 574 MET cc_start: 0.7843 (mmm) cc_final: 0.7245 (tpt) REVERT: B 663 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7622 (ttt180) REVERT: B 678 MET cc_start: 0.2303 (mmt) cc_final: 0.0451 (ttt) REVERT: C 62 MET cc_start: 0.8268 (ttm) cc_final: 0.7943 (ttp) outliers start: 2 outliers final: 2 residues processed: 330 average time/residue: 0.1169 time to fit residues: 57.2912 Evaluate side-chains 285 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124662 restraints weight = 25619.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127763 restraints weight = 14704.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129858 restraints weight = 9949.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131202 restraints weight = 7587.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132053 restraints weight = 6329.125| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14441 Z= 0.125 Angle : 0.617 9.935 19533 Z= 0.315 Chirality : 0.043 0.268 2142 Planarity : 0.004 0.057 2391 Dihedral : 12.242 164.181 2227 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -1.13 (0.21), residues: 1653 helix: 0.72 (0.19), residues: 734 sheet: -0.57 (0.49), residues: 123 loop : -2.29 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.020 0.001 TYR B 685 PHE 0.015 0.001 PHE A 12 TRP 0.016 0.001 TRP A 357 HIS 0.004 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00276 (14441) covalent geometry : angle 0.61749 (19533) hydrogen bonds : bond 0.03775 ( 583) hydrogen bonds : angle 4.49109 ( 1618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7607 (ttp80) cc_final: 0.6646 (ptp90) REVERT: A 22 GLU cc_start: 0.8556 (mp0) cc_final: 0.8298 (mp0) REVERT: A 43 GLN cc_start: 0.8460 (tp40) cc_final: 0.8215 (tp40) REVERT: A 350 LYS cc_start: 0.8515 (tttt) cc_final: 0.8231 (ttpp) REVERT: A 365 PHE cc_start: 0.6997 (t80) cc_final: 0.6678 (t80) REVERT: A 428 GLU cc_start: 0.8193 (tp30) cc_final: 0.7824 (tp30) REVERT: A 497 MET cc_start: 0.8247 (mpp) cc_final: 0.7581 (mmt) REVERT: A 511 ASN cc_start: 0.8855 (t0) cc_final: 0.8450 (t0) REVERT: A 514 LYS cc_start: 0.9131 (tttt) cc_final: 0.8698 (ttpt) REVERT: A 516 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 561 ASP cc_start: 0.8441 (t70) cc_final: 0.8058 (t70) REVERT: A 565 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8724 (mttm) REVERT: A 574 MET cc_start: 0.8482 (mmm) cc_final: 0.8180 (mmm) REVERT: A 619 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8118 (mmtp) REVERT: A 624 CYS cc_start: 0.8791 (p) cc_final: 0.7997 (t) REVERT: B 1 MET cc_start: 0.7293 (tmm) cc_final: 0.6689 (tmm) REVERT: B 79 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8061 (mm-30) REVERT: B 123 SER cc_start: 0.8173 (p) cc_final: 0.7884 (p) REVERT: B 130 GLN cc_start: 0.8547 (tp-100) cc_final: 0.7919 (tp-100) REVERT: B 176 MET cc_start: 0.8525 (mtp) cc_final: 0.8315 (mtm) REVERT: B 220 ILE cc_start: 0.9330 (mm) cc_final: 0.9074 (tp) REVERT: B 254 SER cc_start: 0.9247 (p) cc_final: 0.8708 (t) REVERT: B 289 SER cc_start: 0.8847 (m) cc_final: 0.8519 (p) REVERT: B 336 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8086 (mtpp) REVERT: B 341 VAL cc_start: 0.7825 (p) cc_final: 0.7563 (p) REVERT: B 415 MET cc_start: 0.7388 (mtt) cc_final: 0.7162 (mtt) REVERT: B 428 ARG cc_start: 0.7534 (mmp-170) cc_final: 0.6432 (mmt90) REVERT: B 442 LEU cc_start: 0.8575 (tp) cc_final: 0.8250 (mp) REVERT: B 490 LEU cc_start: 0.8904 (tp) cc_final: 0.8437 (tp) REVERT: B 519 ASN cc_start: 0.8565 (t0) cc_final: 0.7985 (t0) REVERT: B 522 THR cc_start: 0.9215 (p) cc_final: 0.8887 (t) REVERT: B 547 MET cc_start: 0.8296 (ttm) cc_final: 0.7808 (ttm) REVERT: B 574 MET cc_start: 0.7857 (mmm) cc_final: 0.7063 (tpt) REVERT: B 663 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7478 (ttt180) REVERT: B 678 MET cc_start: 0.2087 (mmt) cc_final: 0.0325 (ttt) REVERT: C 62 MET cc_start: 0.8223 (ttm) cc_final: 0.7693 (ttp) REVERT: C 171 MET cc_start: 0.7471 (mtp) cc_final: 0.6522 (ptp) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1088 time to fit residues: 54.6621 Evaluate side-chains 284 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 170 ASN A 296 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124044 restraints weight = 25836.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125663 restraints weight = 14223.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126860 restraints weight = 10284.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127987 restraints weight = 8588.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128261 restraints weight = 7248.960| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14441 Z= 0.143 Angle : 0.638 8.746 19533 Z= 0.329 Chirality : 0.043 0.256 2142 Planarity : 0.004 0.058 2391 Dihedral : 12.271 164.337 2227 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.56 % Rotamer: Outliers : 0.27 % Allowed : 0.34 % Favored : 99.39 % 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: -1.14 (0.21), residues: 1653 helix: 0.72 (0.19), residues: 734 sheet: -0.71 (0.49), residues: 124 loop : -2.29 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.025 0.001 TYR B 685 PHE 0.017 0.001 PHE C 35 TRP 0.029 0.001 TRP A 357 HIS 0.009 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00323 (14441) covalent geometry : angle 0.63785 (19533) hydrogen bonds : bond 0.04064 ( 583) hydrogen bonds : angle 4.55224 ( 1618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 327 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7655 (ttp80) cc_final: 0.6809 (ptp90) REVERT: A 23 GLU cc_start: 0.8582 (tt0) cc_final: 0.8183 (mt-10) REVERT: A 43 GLN cc_start: 0.8432 (tp40) cc_final: 0.8173 (tp40) REVERT: A 235 ARG cc_start: 0.6604 (tpm170) cc_final: 0.6183 (tpm170) REVERT: A 350 LYS cc_start: 0.8506 (tttt) cc_final: 0.8195 (ttpp) REVERT: A 428 GLU cc_start: 0.8138 (tp30) cc_final: 0.7728 (tp30) REVERT: A 497 MET cc_start: 0.8243 (mpp) cc_final: 0.7565 (mmt) REVERT: A 508 GLU cc_start: 0.7802 (tt0) cc_final: 0.7584 (tt0) REVERT: A 511 ASN cc_start: 0.8902 (t0) cc_final: 0.8521 (t0) REVERT: A 514 LYS cc_start: 0.9133 (tttt) cc_final: 0.8612 (tttm) REVERT: A 516 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 565 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8518 (mtmm) REVERT: A 574 MET cc_start: 0.8558 (mmm) cc_final: 0.8148 (mmm) REVERT: A 579 GLN cc_start: 0.8949 (tt0) cc_final: 0.8708 (pp30) REVERT: A 619 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8215 (mmtp) REVERT: B 130 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8207 (tp-100) REVERT: B 176 MET cc_start: 0.8576 (mtp) cc_final: 0.8364 (mtm) REVERT: B 220 ILE cc_start: 0.9352 (mm) cc_final: 0.9043 (tp) REVERT: B 254 SER cc_start: 0.9288 (p) cc_final: 0.8740 (t) REVERT: B 289 SER cc_start: 0.9075 (m) cc_final: 0.8684 (p) REVERT: B 336 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7901 (mtpp) REVERT: B 341 VAL cc_start: 0.7929 (p) cc_final: 0.7646 (p) REVERT: B 353 MET cc_start: 0.8326 (mmp) cc_final: 0.8083 (mmp) REVERT: B 415 MET cc_start: 0.7423 (mtt) cc_final: 0.7198 (mtt) REVERT: B 428 ARG cc_start: 0.7537 (mmp-170) cc_final: 0.6418 (mmt90) REVERT: B 442 LEU cc_start: 0.8596 (tp) cc_final: 0.8259 (mp) REVERT: B 465 LEU cc_start: 0.9224 (mm) cc_final: 0.8960 (mm) REVERT: B 490 LEU cc_start: 0.8921 (tp) cc_final: 0.8484 (tp) REVERT: B 519 ASN cc_start: 0.8641 (t0) cc_final: 0.7948 (t0) REVERT: B 522 THR cc_start: 0.9229 (p) cc_final: 0.8948 (t) REVERT: B 574 MET cc_start: 0.7909 (mmm) cc_final: 0.7325 (tpt) REVERT: B 663 ARG cc_start: 0.7989 (ttp-170) cc_final: 0.7518 (ttt180) REVERT: B 678 MET cc_start: 0.1337 (mmt) cc_final: -0.0263 (ttt) REVERT: B 738 GLU cc_start: 0.8506 (pt0) cc_final: 0.8127 (pp20) REVERT: B 742 LEU cc_start: 0.9298 (mt) cc_final: 0.9026 (mt) REVERT: C 62 MET cc_start: 0.8245 (ttm) cc_final: 0.8035 (ttp) REVERT: C 171 MET cc_start: 0.7451 (mtp) cc_final: 0.6455 (ptp) REVERT: C 739 PHE cc_start: 0.7873 (t80) cc_final: 0.7525 (t80) outliers start: 4 outliers final: 0 residues processed: 329 average time/residue: 0.1093 time to fit residues: 53.7085 Evaluate side-chains 276 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 0.0170 chunk 133 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 141 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127439 restraints weight = 25706.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129012 restraints weight = 14779.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130637 restraints weight = 10486.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131765 restraints weight = 8182.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131850 restraints weight = 7060.513| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14441 Z= 0.114 Angle : 0.621 9.928 19533 Z= 0.317 Chirality : 0.043 0.264 2142 Planarity : 0.004 0.058 2391 Dihedral : 12.221 163.943 2227 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Rotamer: Outliers : 0.14 % Allowed : 0.20 % Favored : 99.66 % 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: -1.08 (0.21), residues: 1653 helix: 0.75 (0.20), residues: 739 sheet: -0.61 (0.48), residues: 123 loop : -2.26 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.026 0.001 TYR B 685 PHE 0.018 0.001 PHE A 652 TRP 0.027 0.001 TRP A 357 HIS 0.003 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00247 (14441) covalent geometry : angle 0.62111 (19533) hydrogen bonds : bond 0.03726 ( 583) hydrogen bonds : angle 4.46465 ( 1618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.14 seconds wall clock time: 40 minutes 50.84 seconds (2450.84 seconds total)