Starting phenix.real_space_refine on Sat Aug 23 17:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kv5_9577/08_2025/6kv5_9577_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kv5_9577/08_2025/6kv5_9577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kv5_9577/08_2025/6kv5_9577_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kv5_9577/08_2025/6kv5_9577_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kv5_9577/08_2025/6kv5_9577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kv5_9577/08_2025/6kv5_9577.map" } resolution = 4.6 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= 0.007 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: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 8604 2.51 5 N 2306 2.21 5 O 2506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13532 Number of models: 1 Model: "" Number of chains: 3 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 Time building chain proxies: 3.38, per 1000 atoms: 0.25 Number of scatterers: 13532 At special positions: 0 Unit cell: (115.6, 108.8, 126.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 2506 8.00 N 2306 7.00 C 8604 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: 1.10 Conformation dependent library (CDL) restraints added in 655.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 14 sheets defined 45.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.636A pdb=" N ILE A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.647A pdb=" N ILE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.893A 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: 4.432A pdb=" N THR A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.633A 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: 3.530A pdb=" N ALA A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.131A 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: 3.798A 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: 3.565A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 569 through 589 removed outlier: 3.872A 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: 3.786A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.597A pdb=" N CYS A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.630A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.518A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 48 removed outlier: 3.907A 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 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 142 through 157 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.517A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 4.126A pdb=" N CYS B 314 " --> pdb=" O TRP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.937A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.709A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.732A 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: 3.575A 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 524 through 538 Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.613A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.670A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.678A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 679 through 696 removed outlier: 3.831A pdb=" N LYS B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 4.666A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.557A pdb=" N TYR B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 3.670A 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 removed outlier: 3.505A pdb=" N CYS C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) 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: 3.605A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.577A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 218 removed outlier: 3.783A pdb=" N PHE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.817A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 727 removed outlier: 3.533A pdb=" N LEU C 727 " --> pdb=" O ARG C 724 " (cutoff:3.500A) 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 107 through 109 removed outlier: 6.454A 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: 5.635A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 7.009A 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: 3.584A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.775A 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 130 through 133 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.676A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.515A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AB5, first strand: chain 'C' and resid 736 through 740 564 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.48 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: 4294 1.34 - 1.46: 2535 1.46 - 1.58: 6775 1.58 - 1.70: 0 1.70 - 1.81: 191 Bond restraints: 13795 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.375 -0.041 8.40e-03 1.42e+04 2.41e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.27e-02 6.20e+03 1.23e+01 bond pdb=" C LEU B 487 " pdb=" N PRO B 488 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 bond pdb=" C ASP C 716 " pdb=" N PRO C 717 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.22e-02 6.72e+03 2.86e+00 bond pdb=" C LEU B 510 " pdb=" N PRO B 511 " ideal model delta sigma weight residual 1.337 1.352 -0.015 9.80e-03 1.04e+04 2.41e+00 ... (remaining 13790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18012 2.09 - 4.19: 441 4.19 - 6.28: 50 6.28 - 8.37: 21 8.37 - 10.47: 5 Bond angle restraints: 18529 Sorted by residual: angle pdb=" CA ILE C 186 " pdb=" CB ILE C 186 " pdb=" CG2 ILE C 186 " ideal model delta sigma weight residual 110.50 117.57 -7.07 1.70e+00 3.46e-01 1.73e+01 angle pdb=" N TYR A 708 " pdb=" CA TYR A 708 " pdb=" C TYR A 708 " ideal model delta sigma weight residual 108.34 113.72 -5.38 1.31e+00 5.83e-01 1.69e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 121.75 -7.65 2.00e+00 2.50e-01 1.46e+01 angle pdb=" C PRO A 202 " pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 120.09 124.59 -4.50 1.25e+00 6.40e-01 1.30e+01 angle pdb=" CA GLN A 358 " pdb=" CB GLN A 358 " pdb=" CG GLN A 358 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 ... (remaining 18524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 8030 14.82 - 29.64: 324 29.64 - 44.47: 99 44.47 - 59.29: 8 59.29 - 74.11: 5 Dihedral angle restraints: 8466 sinusoidal: 3572 harmonic: 4894 Sorted by residual: 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 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+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 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASP C 716 " pdb=" C ASP C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 8463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1890 0.097 - 0.193: 109 0.193 - 0.290: 7 0.290 - 0.387: 0 0.387 - 0.483: 1 Chirality restraints: 2007 Sorted by residual: 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 2.16 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA ASP C 716 " pdb=" N ASP C 716 " pdb=" C ASP C 716 " pdb=" CB ASP C 716 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+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 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2004 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C VAL A 40 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 40 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS A 41 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 38 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C VAL A 38 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 38 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY A 39 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 36 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ILE A 36 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 36 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 37 " -0.014 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1803 2.76 - 3.29: 12574 3.29 - 3.83: 20768 3.83 - 4.36: 24876 4.36 - 4.90: 42150 Nonbonded interactions: 102171 Sorted by model distance: nonbonded pdb=" OE1 GLU C 221 " pdb=" NH2 ARG C 223 " model vdw 2.225 3.120 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.236 3.120 nonbonded pdb=" OG SER A 113 " pdb=" OG1 THR A 134 " model vdw 2.250 3.040 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.272 3.040 nonbonded pdb=" O ASN A 78 " pdb=" OG SER A 82 " model vdw 2.285 3.040 ... (remaining 102166 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.910 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13795 Z= 0.193 Angle : 0.822 10.466 18529 Z= 0.455 Chirality : 0.051 0.483 2007 Planarity : 0.006 0.056 2364 Dihedral : 9.592 74.109 5290 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.59 % Favored : 91.29 % Rotamer: Outliers : 0.41 % Allowed : 2.37 % Favored : 97.23 % 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 aren not related in a simple way. whole: -4.90 (0.15), residues: 1653 helix: -3.40 (0.12), residues: 715 sheet: -1.73 (0.45), residues: 139 loop : -3.39 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 723 TYR 0.021 0.002 TYR A 289 PHE 0.023 0.002 PHE A 161 TRP 0.026 0.003 TRP C 38 HIS 0.007 0.002 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00374 (13795) covalent geometry : angle 0.82226 (18529) hydrogen bonds : bond 0.13787 ( 564) hydrogen bonds : angle 10.11991 ( 1593) *********************** 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 586 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 580 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8492 (t80) cc_final: 0.8065 (m-80) REVERT: A 171 MET cc_start: 0.8263 (mtm) cc_final: 0.7474 (mtm) REVERT: A 173 THR cc_start: 0.8839 (p) cc_final: 0.8334 (p) REVERT: A 208 TYR cc_start: 0.9241 (t80) cc_final: 0.9038 (t80) REVERT: A 228 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8539 (ptmm) REVERT: A 269 ASP cc_start: 0.8050 (m-30) cc_final: 0.7679 (t70) REVERT: A 318 LEU cc_start: 0.9138 (tp) cc_final: 0.8932 (mp) REVERT: A 319 TRP cc_start: 0.8493 (t-100) cc_final: 0.8086 (t-100) REVERT: A 323 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8255 (ptpt) REVERT: A 382 PHE cc_start: 0.8067 (t80) cc_final: 0.7160 (t80) REVERT: A 447 ILE cc_start: 0.9433 (mt) cc_final: 0.9070 (mt) REVERT: A 467 TYR cc_start: 0.8279 (p90) cc_final: 0.7937 (p90) REVERT: A 565 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8289 (mmmm) REVERT: A 575 GLU cc_start: 0.9283 (tt0) cc_final: 0.9079 (tt0) REVERT: A 606 HIS cc_start: 0.7287 (p90) cc_final: 0.6877 (p90) REVERT: A 622 ASP cc_start: 0.9010 (m-30) cc_final: 0.8214 (p0) REVERT: A 624 CYS cc_start: 0.9476 (p) cc_final: 0.8994 (p) REVERT: A 628 ILE cc_start: 0.9164 (tp) cc_final: 0.8821 (tp) REVERT: A 631 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8748 (mm-40) REVERT: A 643 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8191 (mm-30) REVERT: A 645 PHE cc_start: 0.8974 (t80) cc_final: 0.8325 (t80) REVERT: A 651 LYS cc_start: 0.9408 (mtpm) cc_final: 0.8948 (mttt) REVERT: A 659 ASP cc_start: 0.8995 (t70) cc_final: 0.8684 (t0) REVERT: A 669 ASN cc_start: 0.8677 (t0) cc_final: 0.8370 (t0) REVERT: A 684 ASN cc_start: 0.9453 (t0) cc_final: 0.9167 (t0) REVERT: B 41 GLU cc_start: 0.8860 (tt0) cc_final: 0.8224 (tm-30) REVERT: B 45 ARG cc_start: 0.8545 (ttp-170) cc_final: 0.8066 (ttp-170) REVERT: B 91 LEU cc_start: 0.9344 (mt) cc_final: 0.8954 (mt) REVERT: B 96 MET cc_start: 0.8209 (ttm) cc_final: 0.7615 (ttm) REVERT: B 132 TYR cc_start: 0.8392 (t80) cc_final: 0.8188 (t80) REVERT: B 248 MET cc_start: 0.8169 (tpp) cc_final: 0.7632 (tpp) REVERT: B 250 ILE cc_start: 0.8786 (mt) cc_final: 0.8409 (mt) REVERT: B 326 TYR cc_start: 0.8449 (t80) cc_final: 0.8001 (t80) REVERT: B 353 MET cc_start: 0.7687 (mmm) cc_final: 0.7259 (mpp) REVERT: B 390 PHE cc_start: 0.8553 (t80) cc_final: 0.8301 (t80) REVERT: B 403 PHE cc_start: 0.8201 (t80) cc_final: 0.7544 (t80) REVERT: B 416 LEU cc_start: 0.8787 (tp) cc_final: 0.8460 (tp) REVERT: B 423 MET cc_start: 0.7997 (mtp) cc_final: 0.7652 (ttm) REVERT: B 426 ASN cc_start: 0.9126 (m-40) cc_final: 0.8472 (m110) REVERT: B 491 PHE cc_start: 0.8384 (p90) cc_final: 0.8164 (p90) REVERT: B 513 PHE cc_start: 0.6850 (m-10) cc_final: 0.6599 (m-80) REVERT: B 528 MET cc_start: 0.7311 (mtm) cc_final: 0.6675 (mtm) REVERT: B 581 ILE cc_start: 0.8999 (tp) cc_final: 0.8624 (tp) REVERT: B 692 TYR cc_start: 0.8711 (t80) cc_final: 0.8044 (t80) REVERT: B 702 ASN cc_start: 0.7913 (t0) cc_final: 0.7655 (t0) REVERT: B 710 MET cc_start: 0.8252 (mtp) cc_final: 0.7241 (mtp) REVERT: B 714 ILE cc_start: 0.9369 (mt) cc_final: 0.8829 (mt) REVERT: C 103 THR cc_start: 0.9477 (t) cc_final: 0.8955 (t) REVERT: C 130 GLU cc_start: 0.8939 (tt0) cc_final: 0.8520 (tp30) REVERT: C 726 ASP cc_start: 0.8415 (m-30) cc_final: 0.7944 (t70) outliers start: 6 outliers final: 2 residues processed: 586 average time/residue: 0.1506 time to fit residues: 119.3677 Evaluate side-chains 360 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 126 ASN A 263 HIS A 321 GLN A 638 ASN B 32 HIS B 70 ASN B 154 GLN B 477 ASN B 563 HIS ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.133807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104668 restraints weight = 40588.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.107840 restraints weight = 27553.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.110022 restraints weight = 20385.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.111747 restraints weight = 16178.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.112864 restraints weight = 13443.278| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13795 Z= 0.148 Angle : 0.681 11.277 18529 Z= 0.352 Chirality : 0.044 0.212 2007 Planarity : 0.005 0.052 2364 Dihedral : 5.120 23.580 1813 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % 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 aren not related in a simple way. whole: -3.13 (0.18), residues: 1653 helix: -1.38 (0.16), residues: 751 sheet: -1.16 (0.49), residues: 128 loop : -3.00 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 748 TYR 0.016 0.001 TYR A 205 PHE 0.024 0.002 PHE B 219 TRP 0.025 0.002 TRP A 386 HIS 0.006 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00312 (13795) covalent geometry : angle 0.68059 (18529) hydrogen bonds : bond 0.04785 ( 564) hydrogen bonds : angle 5.93912 ( 1593) *********************** 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 416 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 TYR cc_start: 0.8390 (t80) cc_final: 0.7444 (m-80) REVERT: A 168 LYS cc_start: 0.9487 (tppt) cc_final: 0.9059 (tppp) REVERT: A 169 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9074 (mm-30) REVERT: A 269 ASP cc_start: 0.7729 (m-30) cc_final: 0.7448 (t70) REVERT: A 319 TRP cc_start: 0.8689 (t-100) cc_final: 0.8151 (t-100) REVERT: A 357 TRP cc_start: 0.7872 (t60) cc_final: 0.7392 (t60) REVERT: A 382 PHE cc_start: 0.7525 (t80) cc_final: 0.6466 (t80) REVERT: A 447 ILE cc_start: 0.9456 (mt) cc_final: 0.9118 (tt) REVERT: A 467 TYR cc_start: 0.8080 (p90) cc_final: 0.7744 (p90) REVERT: A 480 LEU cc_start: 0.8451 (tp) cc_final: 0.8177 (tp) REVERT: A 497 MET cc_start: 0.5710 (mmp) cc_final: 0.5307 (mtt) REVERT: A 503 PHE cc_start: 0.5624 (m-10) cc_final: 0.4981 (m-10) REVERT: A 555 MET cc_start: 0.8220 (mmp) cc_final: 0.7787 (mmp) REVERT: A 559 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9287 (mmmm) REVERT: A 568 ARG cc_start: 0.7615 (mpp-170) cc_final: 0.7150 (mpp-170) REVERT: A 574 MET cc_start: 0.7488 (ttt) cc_final: 0.6612 (ttt) REVERT: A 606 HIS cc_start: 0.7734 (p90) cc_final: 0.7144 (p90) REVERT: A 622 ASP cc_start: 0.8606 (m-30) cc_final: 0.8288 (p0) REVERT: A 643 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 645 PHE cc_start: 0.8779 (t80) cc_final: 0.7971 (t80) REVERT: A 649 GLN cc_start: 0.9427 (pt0) cc_final: 0.9056 (pt0) REVERT: A 669 ASN cc_start: 0.8616 (t0) cc_final: 0.8249 (t0) REVERT: A 697 LEU cc_start: 0.9504 (tp) cc_final: 0.9301 (tp) REVERT: B 14 ILE cc_start: 0.9226 (mm) cc_final: 0.8956 (mm) REVERT: B 41 GLU cc_start: 0.8870 (tt0) cc_final: 0.8376 (tm-30) REVERT: B 45 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.8174 (ttp-170) REVERT: B 87 ILE cc_start: 0.9120 (pt) cc_final: 0.8644 (pt) REVERT: B 91 LEU cc_start: 0.9205 (mt) cc_final: 0.8765 (mt) REVERT: B 160 PHE cc_start: 0.8198 (t80) cc_final: 0.5855 (t80) REVERT: B 226 ILE cc_start: 0.7898 (mp) cc_final: 0.7456 (mp) REVERT: B 248 MET cc_start: 0.8255 (tpp) cc_final: 0.7611 (tpp) REVERT: B 326 TYR cc_start: 0.8498 (t80) cc_final: 0.8283 (t80) REVERT: B 335 MET cc_start: 0.8642 (mmt) cc_final: 0.8389 (ptm) REVERT: B 346 PHE cc_start: 0.8540 (m-10) cc_final: 0.8241 (m-10) REVERT: B 353 MET cc_start: 0.7491 (mmm) cc_final: 0.7263 (mtt) REVERT: B 366 LYS cc_start: 0.7782 (pttt) cc_final: 0.6434 (mmtt) REVERT: B 390 PHE cc_start: 0.8899 (t80) cc_final: 0.8517 (t80) REVERT: B 403 PHE cc_start: 0.8096 (t80) cc_final: 0.7626 (t80) REVERT: B 416 LEU cc_start: 0.8617 (tp) cc_final: 0.8376 (tp) REVERT: B 423 MET cc_start: 0.8053 (mtp) cc_final: 0.7437 (ttm) REVERT: B 426 ASN cc_start: 0.9242 (m-40) cc_final: 0.8599 (m110) REVERT: B 446 ASP cc_start: 0.8297 (p0) cc_final: 0.8071 (p0) REVERT: B 449 VAL cc_start: 0.8947 (t) cc_final: 0.8704 (p) REVERT: B 450 LEU cc_start: 0.8928 (tp) cc_final: 0.8662 (tp) REVERT: B 462 MET cc_start: 0.9051 (mmp) cc_final: 0.8702 (tpp) REVERT: B 466 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9217 (mtmm) REVERT: B 482 LYS cc_start: 0.9339 (mtmt) cc_final: 0.9117 (mttt) REVERT: B 513 PHE cc_start: 0.7163 (m-10) cc_final: 0.6732 (m-10) REVERT: B 544 THR cc_start: 0.8620 (p) cc_final: 0.7590 (p) REVERT: B 611 ILE cc_start: 0.9587 (mt) cc_final: 0.9301 (tt) REVERT: B 665 ARG cc_start: 0.7486 (tpt90) cc_final: 0.6720 (tpp80) REVERT: B 702 ASN cc_start: 0.7708 (t0) cc_final: 0.7239 (m-40) REVERT: C 81 ASP cc_start: 0.7802 (t0) cc_final: 0.7493 (t0) REVERT: C 107 PHE cc_start: 0.8649 (m-80) cc_final: 0.8404 (m-80) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.1300 time to fit residues: 75.6394 Evaluate side-chains 323 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 114 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 165 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 638 ASN B 315 GLN C 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104860 restraints weight = 41363.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108176 restraints weight = 27493.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.110534 restraints weight = 20152.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112095 restraints weight = 15886.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113386 restraints weight = 13304.925| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13795 Z= 0.127 Angle : 0.647 8.698 18529 Z= 0.332 Chirality : 0.043 0.172 2007 Planarity : 0.005 0.092 2364 Dihedral : 4.847 18.857 1813 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % 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 aren not related in a simple way. whole: -2.47 (0.19), residues: 1653 helix: -0.75 (0.18), residues: 746 sheet: -1.05 (0.48), residues: 128 loop : -2.68 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 11 TYR 0.018 0.001 TYR B 560 PHE 0.018 0.001 PHE C 212 TRP 0.050 0.002 TRP B 178 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00272 (13795) covalent geometry : angle 0.64710 (18529) hydrogen bonds : bond 0.04334 ( 564) hydrogen bonds : angle 5.35004 ( 1593) *********************** 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 406 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8261 (t80) cc_final: 0.7288 (m-80) REVERT: A 208 TYR cc_start: 0.8675 (t80) cc_final: 0.8320 (t80) REVERT: A 222 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7877 (pm20) REVERT: A 252 GLU cc_start: 0.7632 (tp30) cc_final: 0.7414 (tp30) REVERT: A 269 ASP cc_start: 0.7978 (m-30) cc_final: 0.7583 (t70) REVERT: A 323 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7421 (mtpp) REVERT: A 357 TRP cc_start: 0.7834 (t60) cc_final: 0.7454 (t60) REVERT: A 382 PHE cc_start: 0.7555 (t80) cc_final: 0.6871 (t80) REVERT: A 403 TRP cc_start: 0.8636 (m-90) cc_final: 0.7876 (m-90) REVERT: A 406 MET cc_start: 0.9242 (tpt) cc_final: 0.8566 (tpt) REVERT: A 409 MET cc_start: 0.7916 (tpp) cc_final: 0.7695 (tpp) REVERT: A 413 LYS cc_start: 0.8550 (mppt) cc_final: 0.8185 (mtmm) REVERT: A 447 ILE cc_start: 0.9487 (mt) cc_final: 0.9143 (tt) REVERT: A 467 TYR cc_start: 0.8163 (p90) cc_final: 0.7791 (p90) REVERT: A 497 MET cc_start: 0.5643 (mmp) cc_final: 0.5285 (mtt) REVERT: A 503 PHE cc_start: 0.4980 (m-10) cc_final: 0.4617 (m-10) REVERT: A 555 MET cc_start: 0.8299 (mmp) cc_final: 0.7996 (mmm) REVERT: A 574 MET cc_start: 0.7547 (ttt) cc_final: 0.6395 (ttt) REVERT: A 583 LYS cc_start: 0.9011 (ptpp) cc_final: 0.8808 (pttm) REVERT: A 606 HIS cc_start: 0.7712 (p90) cc_final: 0.6818 (p90) REVERT: A 622 ASP cc_start: 0.8905 (m-30) cc_final: 0.8102 (p0) REVERT: A 628 ILE cc_start: 0.9303 (tp) cc_final: 0.9024 (tp) REVERT: A 643 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 645 PHE cc_start: 0.8660 (t80) cc_final: 0.8060 (t80) REVERT: A 649 GLN cc_start: 0.9417 (pt0) cc_final: 0.9095 (pt0) REVERT: A 651 LYS cc_start: 0.9338 (tppp) cc_final: 0.8761 (mttt) REVERT: A 669 ASN cc_start: 0.8649 (t0) cc_final: 0.8218 (t0) REVERT: A 684 ASN cc_start: 0.9511 (t0) cc_final: 0.9290 (t0) REVERT: B 4 ASN cc_start: 0.9221 (t0) cc_final: 0.9007 (t0) REVERT: B 41 GLU cc_start: 0.8975 (tt0) cc_final: 0.8545 (tm-30) REVERT: B 45 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.7295 (ttp-170) REVERT: B 49 TYR cc_start: 0.8957 (m-10) cc_final: 0.8661 (m-80) REVERT: B 185 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8357 (pttp) REVERT: B 210 MET cc_start: 0.6489 (pmm) cc_final: 0.5839 (pmm) REVERT: B 248 MET cc_start: 0.8294 (tpp) cc_final: 0.7622 (tpp) REVERT: B 353 MET cc_start: 0.7464 (mmm) cc_final: 0.7263 (mpp) REVERT: B 390 PHE cc_start: 0.8945 (t80) cc_final: 0.8601 (t80) REVERT: B 403 PHE cc_start: 0.8022 (t80) cc_final: 0.7632 (t80) REVERT: B 426 ASN cc_start: 0.9157 (m-40) cc_final: 0.8491 (m110) REVERT: B 449 VAL cc_start: 0.8757 (t) cc_final: 0.8530 (p) REVERT: B 450 LEU cc_start: 0.8954 (tp) cc_final: 0.8647 (tp) REVERT: B 462 MET cc_start: 0.9094 (mmp) cc_final: 0.8789 (tpp) REVERT: B 466 LYS cc_start: 0.9604 (mmmt) cc_final: 0.9315 (mtmm) REVERT: B 481 GLU cc_start: 0.8173 (mp0) cc_final: 0.7842 (mp0) REVERT: B 482 LYS cc_start: 0.9454 (mtmt) cc_final: 0.8534 (mttt) REVERT: B 491 PHE cc_start: 0.8351 (p90) cc_final: 0.7781 (p90) REVERT: B 494 THR cc_start: 0.7473 (p) cc_final: 0.7256 (p) REVERT: B 502 PHE cc_start: 0.8677 (m-80) cc_final: 0.8235 (m-10) REVERT: B 513 PHE cc_start: 0.7004 (m-10) cc_final: 0.6606 (m-10) REVERT: B 544 THR cc_start: 0.8526 (p) cc_final: 0.7713 (p) REVERT: B 611 ILE cc_start: 0.9665 (mt) cc_final: 0.9347 (tt) REVERT: B 665 ARG cc_start: 0.7703 (tpt90) cc_final: 0.7000 (tpp80) REVERT: B 702 ASN cc_start: 0.7659 (t0) cc_final: 0.7345 (m110) REVERT: B 708 MET cc_start: 0.4707 (pmm) cc_final: 0.4039 (ptt) REVERT: B 736 TYR cc_start: 0.9061 (t80) cc_final: 0.8791 (t80) REVERT: C 7 LEU cc_start: 0.8654 (mm) cc_final: 0.8209 (mm) REVERT: C 10 GLU cc_start: 0.9127 (pt0) cc_final: 0.8659 (pp20) REVERT: C 81 ASP cc_start: 0.8024 (t0) cc_final: 0.7812 (t0) REVERT: C 134 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7664 (pp20) REVERT: C 213 MET cc_start: 0.6942 (ptt) cc_final: 0.6736 (ptt) outliers start: 1 outliers final: 1 residues processed: 406 average time/residue: 0.1107 time to fit residues: 64.3328 Evaluate side-chains 325 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.132734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105450 restraints weight = 41755.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108186 restraints weight = 29085.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110632 restraints weight = 20153.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111064 restraints weight = 16420.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.111510 restraints weight = 15371.370| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13795 Z= 0.139 Angle : 0.656 10.654 18529 Z= 0.335 Chirality : 0.044 0.226 2007 Planarity : 0.005 0.065 2364 Dihedral : 4.789 19.098 1813 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 aren not related in a simple way. whole: -2.17 (0.20), residues: 1653 helix: -0.40 (0.18), residues: 737 sheet: -0.95 (0.48), residues: 128 loop : -2.61 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 693 TYR 0.012 0.001 TYR A 549 PHE 0.016 0.002 PHE B 696 TRP 0.037 0.002 TRP A 386 HIS 0.009 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00292 (13795) covalent geometry : angle 0.65598 (18529) hydrogen bonds : bond 0.04157 ( 564) hydrogen bonds : angle 5.05055 ( 1593) *********************** 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 396 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 TYR cc_start: 0.8377 (t80) cc_final: 0.7391 (m-80) REVERT: A 208 TYR cc_start: 0.8645 (t80) cc_final: 0.8204 (t80) REVERT: A 222 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8104 (pm20) REVERT: A 269 ASP cc_start: 0.7937 (m-30) cc_final: 0.7462 (t70) REVERT: A 357 TRP cc_start: 0.7970 (t60) cc_final: 0.7475 (t60) REVERT: A 382 PHE cc_start: 0.7851 (t80) cc_final: 0.7448 (t80) REVERT: A 403 TRP cc_start: 0.8867 (m-90) cc_final: 0.7987 (m-90) REVERT: A 406 MET cc_start: 0.9179 (tpt) cc_final: 0.8583 (tpt) REVERT: A 447 ILE cc_start: 0.9571 (mt) cc_final: 0.9240 (tt) REVERT: A 467 TYR cc_start: 0.8112 (p90) cc_final: 0.7776 (p90) REVERT: A 499 THR cc_start: 0.7754 (m) cc_final: 0.7369 (t) REVERT: A 503 PHE cc_start: 0.4963 (m-10) cc_final: 0.4499 (m-10) REVERT: A 560 ASN cc_start: 0.9054 (m-40) cc_final: 0.8794 (m-40) REVERT: A 562 TRP cc_start: 0.8241 (m100) cc_final: 0.7758 (m100) REVERT: A 574 MET cc_start: 0.7399 (ttt) cc_final: 0.6861 (ttt) REVERT: A 606 HIS cc_start: 0.7640 (p90) cc_final: 0.6565 (p-80) REVERT: A 622 ASP cc_start: 0.9012 (m-30) cc_final: 0.8343 (p0) REVERT: A 643 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 645 PHE cc_start: 0.8683 (t80) cc_final: 0.8045 (t80) REVERT: A 649 GLN cc_start: 0.9458 (pt0) cc_final: 0.9194 (pt0) REVERT: A 659 ASP cc_start: 0.9239 (t0) cc_final: 0.8617 (t0) REVERT: A 669 ASN cc_start: 0.8630 (t0) cc_final: 0.8187 (t0) REVERT: A 684 ASN cc_start: 0.9529 (t0) cc_final: 0.9277 (t0) REVERT: B 4 ASN cc_start: 0.9179 (t0) cc_final: 0.8852 (t0) REVERT: B 25 THR cc_start: 0.8869 (p) cc_final: 0.8341 (p) REVERT: B 41 GLU cc_start: 0.8875 (tt0) cc_final: 0.8406 (tm-30) REVERT: B 45 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.7282 (ttp-170) REVERT: B 49 TYR cc_start: 0.8900 (m-10) cc_final: 0.8644 (m-80) REVERT: B 96 MET cc_start: 0.8242 (mmt) cc_final: 0.7948 (mmt) REVERT: B 172 ILE cc_start: 0.9554 (mt) cc_final: 0.9305 (mt) REVERT: B 185 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8444 (pttp) REVERT: B 210 MET cc_start: 0.6593 (pmm) cc_final: 0.6022 (pmm) REVERT: B 248 MET cc_start: 0.8319 (tpp) cc_final: 0.7705 (tpp) REVERT: B 348 ASN cc_start: 0.9056 (p0) cc_final: 0.8271 (t0) REVERT: B 353 MET cc_start: 0.7572 (mmm) cc_final: 0.7317 (mpp) REVERT: B 366 LYS cc_start: 0.7090 (pttp) cc_final: 0.5704 (mmtp) REVERT: B 390 PHE cc_start: 0.8948 (t80) cc_final: 0.8626 (t80) REVERT: B 423 MET cc_start: 0.8214 (mtp) cc_final: 0.7603 (mtt) REVERT: B 426 ASN cc_start: 0.9314 (m-40) cc_final: 0.8731 (m110) REVERT: B 449 VAL cc_start: 0.8808 (t) cc_final: 0.8576 (p) REVERT: B 450 LEU cc_start: 0.8951 (tp) cc_final: 0.8692 (tp) REVERT: B 491 PHE cc_start: 0.8289 (p90) cc_final: 0.7534 (p90) REVERT: B 502 PHE cc_start: 0.8507 (m-80) cc_final: 0.8183 (m-10) REVERT: B 513 PHE cc_start: 0.7431 (m-10) cc_final: 0.6817 (m-10) REVERT: B 544 THR cc_start: 0.8542 (p) cc_final: 0.7748 (p) REVERT: B 665 ARG cc_start: 0.7760 (tpt90) cc_final: 0.7082 (tpp-160) REVERT: B 692 TYR cc_start: 0.8579 (t80) cc_final: 0.8263 (t80) REVERT: C 32 TYR cc_start: 0.7751 (t80) cc_final: 0.7493 (t80) REVERT: C 55 MET cc_start: 0.5026 (mtp) cc_final: 0.3594 (ttm) REVERT: C 126 PHE cc_start: 0.8255 (m-10) cc_final: 0.8039 (m-80) REVERT: C 134 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7557 (pp20) REVERT: C 140 MET cc_start: 0.6519 (mtt) cc_final: 0.3198 (mtt) REVERT: C 142 PHE cc_start: 0.8523 (m-80) cc_final: 0.8212 (m-80) REVERT: C 171 MET cc_start: 0.5467 (tpt) cc_final: 0.5093 (tpt) REVERT: C 726 ASP cc_start: 0.8363 (t70) cc_final: 0.8086 (t0) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1105 time to fit residues: 63.2732 Evaluate side-chains 323 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 161 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 10 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS B 383 ASN B 660 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104847 restraints weight = 41987.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.108173 restraints weight = 27866.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.110601 restraints weight = 20349.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.112284 restraints weight = 15855.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.113588 restraints weight = 13120.812| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13795 Z= 0.118 Angle : 0.642 9.946 18529 Z= 0.324 Chirality : 0.044 0.192 2007 Planarity : 0.005 0.074 2364 Dihedral : 4.700 23.142 1813 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.77 % 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 aren not related in a simple way. whole: -1.97 (0.20), residues: 1653 helix: -0.22 (0.18), residues: 747 sheet: -0.69 (0.50), residues: 118 loop : -2.56 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 693 TYR 0.011 0.001 TYR A 261 PHE 0.029 0.001 PHE A 158 TRP 0.027 0.002 TRP A 386 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00258 (13795) covalent geometry : angle 0.64202 (18529) hydrogen bonds : bond 0.03995 ( 564) hydrogen bonds : angle 4.83404 ( 1593) *********************** 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 400 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 TYR cc_start: 0.8394 (t80) cc_final: 0.7405 (m-80) REVERT: A 208 TYR cc_start: 0.8659 (t80) cc_final: 0.8262 (t80) REVERT: A 222 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8074 (pm20) REVERT: A 242 HIS cc_start: 0.7144 (m-70) cc_final: 0.6800 (m-70) REVERT: A 269 ASP cc_start: 0.8143 (m-30) cc_final: 0.7492 (t70) REVERT: A 297 MET cc_start: 0.9117 (mpp) cc_final: 0.8787 (mpp) REVERT: A 323 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7773 (mtpp) REVERT: A 357 TRP cc_start: 0.7809 (t60) cc_final: 0.7451 (t60) REVERT: A 382 PHE cc_start: 0.8011 (t80) cc_final: 0.7592 (t80) REVERT: A 406 MET cc_start: 0.9065 (tpt) cc_final: 0.8573 (tpt) REVERT: A 467 TYR cc_start: 0.8112 (p90) cc_final: 0.7753 (p90) REVERT: A 499 THR cc_start: 0.7766 (m) cc_final: 0.7428 (t) REVERT: A 503 PHE cc_start: 0.5114 (m-10) cc_final: 0.4639 (m-10) REVERT: A 562 TRP cc_start: 0.8011 (m100) cc_final: 0.7630 (m100) REVERT: A 574 MET cc_start: 0.7275 (ttt) cc_final: 0.7047 (ttt) REVERT: A 583 LYS cc_start: 0.8822 (ptpp) cc_final: 0.8446 (pttp) REVERT: A 606 HIS cc_start: 0.7647 (p90) cc_final: 0.6635 (p-80) REVERT: A 622 ASP cc_start: 0.9034 (m-30) cc_final: 0.8314 (p0) REVERT: A 643 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 645 PHE cc_start: 0.8766 (t80) cc_final: 0.8170 (t80) REVERT: A 649 GLN cc_start: 0.9424 (pt0) cc_final: 0.9205 (pt0) REVERT: A 651 LYS cc_start: 0.9452 (tppt) cc_final: 0.8936 (mttt) REVERT: A 659 ASP cc_start: 0.9236 (t0) cc_final: 0.8854 (t0) REVERT: A 684 ASN cc_start: 0.9512 (t0) cc_final: 0.9266 (t0) REVERT: B 3 ILE cc_start: 0.7389 (tt) cc_final: 0.7028 (tt) REVERT: B 4 ASN cc_start: 0.9019 (t0) cc_final: 0.8721 (t0) REVERT: B 25 THR cc_start: 0.8809 (p) cc_final: 0.8213 (p) REVERT: B 41 GLU cc_start: 0.8812 (tt0) cc_final: 0.8333 (tm-30) REVERT: B 45 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.7313 (ttp-170) REVERT: B 49 TYR cc_start: 0.8927 (m-10) cc_final: 0.8704 (m-80) REVERT: B 96 MET cc_start: 0.8266 (mmt) cc_final: 0.7951 (mmt) REVERT: B 185 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8278 (pttp) REVERT: B 210 MET cc_start: 0.6542 (pmm) cc_final: 0.6110 (pmm) REVERT: B 248 MET cc_start: 0.8245 (tpp) cc_final: 0.7741 (tpp) REVERT: B 366 LYS cc_start: 0.7050 (pttp) cc_final: 0.5703 (mmtt) REVERT: B 403 PHE cc_start: 0.8020 (t80) cc_final: 0.7718 (t80) REVERT: B 426 ASN cc_start: 0.9281 (m-40) cc_final: 0.8686 (m110) REVERT: B 446 ASP cc_start: 0.8314 (p0) cc_final: 0.8017 (p0) REVERT: B 447 ASP cc_start: 0.7871 (m-30) cc_final: 0.7436 (m-30) REVERT: B 449 VAL cc_start: 0.8823 (t) cc_final: 0.8524 (p) REVERT: B 450 LEU cc_start: 0.8900 (tp) cc_final: 0.8641 (tp) REVERT: B 462 MET cc_start: 0.8850 (tpp) cc_final: 0.8589 (tpp) REVERT: B 481 GLU cc_start: 0.8228 (mp0) cc_final: 0.8022 (mt-10) REVERT: B 491 PHE cc_start: 0.8230 (p90) cc_final: 0.7355 (p90) REVERT: B 502 PHE cc_start: 0.8477 (m-80) cc_final: 0.8274 (m-10) REVERT: B 513 PHE cc_start: 0.7358 (m-10) cc_final: 0.6799 (m-10) REVERT: B 518 MET cc_start: 0.6982 (mmp) cc_final: 0.6736 (mmt) REVERT: B 611 ILE cc_start: 0.9627 (mt) cc_final: 0.9329 (tt) REVERT: B 665 ARG cc_start: 0.7725 (tpt90) cc_final: 0.6920 (tpp80) REVERT: B 708 MET cc_start: 0.4319 (pmm) cc_final: 0.4060 (pmm) REVERT: B 710 MET cc_start: 0.7844 (mtp) cc_final: 0.7438 (mtp) REVERT: C 7 LEU cc_start: 0.8774 (mm) cc_final: 0.8384 (mm) REVERT: C 10 GLU cc_start: 0.9220 (pt0) cc_final: 0.8579 (pp20) REVERT: C 32 TYR cc_start: 0.7713 (t80) cc_final: 0.7398 (t80) REVERT: C 55 MET cc_start: 0.5792 (mtp) cc_final: 0.3979 (ttm) REVERT: C 134 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7561 (pp20) REVERT: C 159 ILE cc_start: 0.6412 (mp) cc_final: 0.6130 (pt) REVERT: C 726 ASP cc_start: 0.8381 (t70) cc_final: 0.8051 (t0) outliers start: 1 outliers final: 0 residues processed: 400 average time/residue: 0.1108 time to fit residues: 64.0196 Evaluate side-chains 332 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 0.3980 chunk 152 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 277 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.129913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102763 restraints weight = 43363.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105325 restraints weight = 30393.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107218 restraints weight = 21256.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.107666 restraints weight = 18104.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.108298 restraints weight = 16876.116| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13795 Z= 0.156 Angle : 0.678 11.800 18529 Z= 0.349 Chirality : 0.044 0.185 2007 Planarity : 0.005 0.063 2364 Dihedral : 4.782 23.229 1813 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 aren not related in a simple way. whole: -1.85 (0.20), residues: 1653 helix: -0.03 (0.18), residues: 740 sheet: -0.72 (0.48), residues: 129 loop : -2.58 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 167 TYR 0.014 0.001 TYR A 549 PHE 0.041 0.002 PHE C 126 TRP 0.024 0.002 TRP A 386 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00335 (13795) covalent geometry : angle 0.67790 (18529) hydrogen bonds : bond 0.04108 ( 564) hydrogen bonds : angle 4.88802 ( 1593) *********************** 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 390 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8301 (t80) cc_final: 0.8076 (t80) REVERT: A 116 TYR cc_start: 0.8398 (t80) cc_final: 0.7399 (m-80) REVERT: A 175 MET cc_start: 0.8524 (pmm) cc_final: 0.8249 (pmm) REVERT: A 208 TYR cc_start: 0.8797 (t80) cc_final: 0.8395 (t80) REVERT: A 222 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7669 (pm20) REVERT: A 269 ASP cc_start: 0.8133 (m-30) cc_final: 0.7268 (t0) REVERT: A 297 MET cc_start: 0.9148 (mpp) cc_final: 0.8774 (mpp) REVERT: A 357 TRP cc_start: 0.7895 (t60) cc_final: 0.7420 (t60) REVERT: A 382 PHE cc_start: 0.8182 (t80) cc_final: 0.7738 (t80) REVERT: A 403 TRP cc_start: 0.9020 (m-10) cc_final: 0.8398 (m-10) REVERT: A 406 MET cc_start: 0.9027 (tpt) cc_final: 0.8621 (tpt) REVERT: A 425 GLU cc_start: 0.8748 (pp20) cc_final: 0.8385 (pp20) REVERT: A 426 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8418 (mm-30) REVERT: A 447 ILE cc_start: 0.9518 (mt) cc_final: 0.9076 (tt) REVERT: A 467 TYR cc_start: 0.8125 (p90) cc_final: 0.7762 (p90) REVERT: A 499 THR cc_start: 0.7975 (m) cc_final: 0.7614 (t) REVERT: A 503 PHE cc_start: 0.5240 (m-10) cc_final: 0.4869 (m-10) REVERT: A 559 LYS cc_start: 0.9627 (tppp) cc_final: 0.9091 (mtpt) REVERT: A 560 ASN cc_start: 0.9080 (m-40) cc_final: 0.8751 (m-40) REVERT: A 562 TRP cc_start: 0.8163 (m100) cc_final: 0.7721 (m100) REVERT: A 563 PHE cc_start: 0.9363 (m-80) cc_final: 0.9130 (m-10) REVERT: A 606 HIS cc_start: 0.7921 (p-80) cc_final: 0.7196 (p-80) REVERT: A 622 ASP cc_start: 0.9127 (m-30) cc_final: 0.8424 (p0) REVERT: A 624 CYS cc_start: 0.9153 (p) cc_final: 0.8891 (p) REVERT: A 643 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 645 PHE cc_start: 0.8724 (t80) cc_final: 0.8137 (t80) REVERT: A 651 LYS cc_start: 0.9485 (tppt) cc_final: 0.8717 (mttt) REVERT: A 659 ASP cc_start: 0.9269 (t0) cc_final: 0.8904 (t0) REVERT: A 684 ASN cc_start: 0.9518 (t0) cc_final: 0.9240 (t0) REVERT: B 3 ILE cc_start: 0.7680 (tt) cc_final: 0.7244 (tt) REVERT: B 25 THR cc_start: 0.8939 (p) cc_final: 0.8291 (p) REVERT: B 41 GLU cc_start: 0.8857 (tt0) cc_final: 0.8396 (tm-30) REVERT: B 45 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.7426 (ttm170) REVERT: B 49 TYR cc_start: 0.8957 (m-10) cc_final: 0.8752 (m-80) REVERT: B 96 MET cc_start: 0.8353 (mmt) cc_final: 0.8065 (mmt) REVERT: B 129 ARG cc_start: 0.8741 (ptp90) cc_final: 0.8424 (ptm160) REVERT: B 130 GLN cc_start: 0.8791 (mt0) cc_final: 0.8246 (mm-40) REVERT: B 185 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8365 (pttp) REVERT: B 210 MET cc_start: 0.6666 (pmm) cc_final: 0.6181 (pmm) REVERT: B 240 ARG cc_start: 0.6206 (mtm110) cc_final: 0.5182 (ttp-170) REVERT: B 248 MET cc_start: 0.7980 (tpp) cc_final: 0.7714 (tpp) REVERT: B 348 ASN cc_start: 0.9123 (p0) cc_final: 0.8366 (t0) REVERT: B 426 ASN cc_start: 0.9256 (m-40) cc_final: 0.8711 (m110) REVERT: B 449 VAL cc_start: 0.8828 (t) cc_final: 0.8565 (p) REVERT: B 450 LEU cc_start: 0.9011 (tp) cc_final: 0.8686 (tp) REVERT: B 491 PHE cc_start: 0.8160 (p90) cc_final: 0.7383 (p90) REVERT: B 502 PHE cc_start: 0.8509 (m-80) cc_final: 0.8285 (m-10) REVERT: B 513 PHE cc_start: 0.7540 (m-10) cc_final: 0.6885 (m-10) REVERT: B 544 THR cc_start: 0.8458 (p) cc_final: 0.7719 (p) REVERT: B 665 ARG cc_start: 0.7934 (tpt90) cc_final: 0.7119 (tpp80) REVERT: C 7 LEU cc_start: 0.8906 (mm) cc_final: 0.8387 (mm) REVERT: C 10 GLU cc_start: 0.9215 (pt0) cc_final: 0.8581 (pp20) REVERT: C 55 MET cc_start: 0.5327 (mtp) cc_final: 0.3998 (ttm) REVERT: C 134 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7632 (pp20) REVERT: C 171 MET cc_start: 0.6762 (mmm) cc_final: 0.5989 (mtp) REVERT: C 218 PHE cc_start: 0.8158 (m-10) cc_final: 0.7935 (m-10) REVERT: C 246 PHE cc_start: 0.7888 (m-80) cc_final: 0.7541 (m-80) REVERT: C 726 ASP cc_start: 0.8407 (t70) cc_final: 0.8105 (t0) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.1092 time to fit residues: 60.9417 Evaluate side-chains 331 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 57 optimal weight: 0.0030 chunk 94 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 538 ASN B 660 HIS C 13 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105496 restraints weight = 42333.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.107922 restraints weight = 30608.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.109864 restraints weight = 21677.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110218 restraints weight = 18729.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.110858 restraints weight = 17255.734| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13795 Z= 0.128 Angle : 0.682 11.680 18529 Z= 0.346 Chirality : 0.045 0.191 2007 Planarity : 0.004 0.063 2364 Dihedral : 4.746 23.602 1813 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % 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 aren not related in a simple way. whole: -1.71 (0.20), residues: 1653 helix: 0.09 (0.19), residues: 742 sheet: -0.55 (0.49), residues: 129 loop : -2.53 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 167 TYR 0.018 0.001 TYR B 326 PHE 0.026 0.001 PHE B 253 TRP 0.028 0.002 TRP A 603 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00273 (13795) covalent geometry : angle 0.68169 (18529) hydrogen bonds : bond 0.04143 ( 564) hydrogen bonds : angle 4.84211 ( 1593) *********************** 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 394 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8222 (t80) cc_final: 0.8010 (t80) REVERT: A 208 TYR cc_start: 0.8691 (t80) cc_final: 0.8235 (t80) REVERT: A 269 ASP cc_start: 0.7958 (m-30) cc_final: 0.7319 (t0) REVERT: A 297 MET cc_start: 0.9014 (mpp) cc_final: 0.8724 (mpp) REVERT: A 319 TRP cc_start: 0.8273 (t-100) cc_final: 0.7990 (t-100) REVERT: A 328 ASP cc_start: 0.9042 (m-30) cc_final: 0.8829 (m-30) REVERT: A 357 TRP cc_start: 0.7786 (t60) cc_final: 0.7437 (t60) REVERT: A 382 PHE cc_start: 0.8111 (t80) cc_final: 0.7658 (t80) REVERT: A 403 TRP cc_start: 0.8840 (m-10) cc_final: 0.8369 (m-10) REVERT: A 406 MET cc_start: 0.8857 (tpt) cc_final: 0.8584 (tpt) REVERT: A 425 GLU cc_start: 0.8609 (pp20) cc_final: 0.7806 (pp20) REVERT: A 426 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8165 (mm-30) REVERT: A 467 TYR cc_start: 0.7935 (p90) cc_final: 0.7670 (p90) REVERT: A 499 THR cc_start: 0.8005 (m) cc_final: 0.7705 (t) REVERT: A 503 PHE cc_start: 0.5059 (m-10) cc_final: 0.4661 (m-10) REVERT: A 559 LYS cc_start: 0.9626 (tppp) cc_final: 0.9356 (tppp) REVERT: A 606 HIS cc_start: 0.7897 (p-80) cc_final: 0.7168 (p-80) REVERT: A 624 CYS cc_start: 0.9148 (p) cc_final: 0.8926 (p) REVERT: A 643 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 645 PHE cc_start: 0.8548 (t80) cc_final: 0.7861 (t80) REVERT: A 651 LYS cc_start: 0.9386 (tppt) cc_final: 0.8684 (mttt) REVERT: A 659 ASP cc_start: 0.9197 (t0) cc_final: 0.8862 (t0) REVERT: A 684 ASN cc_start: 0.9451 (t0) cc_final: 0.9194 (t0) REVERT: B 3 ILE cc_start: 0.7880 (tt) cc_final: 0.7539 (tt) REVERT: B 4 ASN cc_start: 0.8928 (t0) cc_final: 0.8551 (t0) REVERT: B 41 GLU cc_start: 0.8770 (tt0) cc_final: 0.8295 (tm-30) REVERT: B 45 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.7165 (ttp-170) REVERT: B 95 GLU cc_start: 0.8193 (tt0) cc_final: 0.7717 (tm-30) REVERT: B 96 MET cc_start: 0.8346 (mmt) cc_final: 0.7574 (mmt) REVERT: B 129 ARG cc_start: 0.8749 (ptp90) cc_final: 0.8432 (ptm160) REVERT: B 132 TYR cc_start: 0.8254 (t80) cc_final: 0.7998 (t80) REVERT: B 140 MET cc_start: 0.8887 (mmm) cc_final: 0.8684 (mmm) REVERT: B 185 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8327 (pttt) REVERT: B 210 MET cc_start: 0.6518 (pmm) cc_final: 0.5857 (pmm) REVERT: B 248 MET cc_start: 0.7877 (tpp) cc_final: 0.7620 (tpp) REVERT: B 348 ASN cc_start: 0.9003 (p0) cc_final: 0.8114 (t0) REVERT: B 381 LEU cc_start: 0.8165 (mp) cc_final: 0.7908 (mp) REVERT: B 423 MET cc_start: 0.8239 (mtt) cc_final: 0.8005 (mtp) REVERT: B 426 ASN cc_start: 0.9264 (m-40) cc_final: 0.8756 (m110) REVERT: B 446 ASP cc_start: 0.8356 (p0) cc_final: 0.7854 (p0) REVERT: B 447 ASP cc_start: 0.7774 (m-30) cc_final: 0.7498 (m-30) REVERT: B 449 VAL cc_start: 0.8738 (t) cc_final: 0.8504 (p) REVERT: B 450 LEU cc_start: 0.8845 (tp) cc_final: 0.8624 (tp) REVERT: B 491 PHE cc_start: 0.7932 (p90) cc_final: 0.7105 (p90) REVERT: B 502 PHE cc_start: 0.8176 (m-80) cc_final: 0.7972 (m-10) REVERT: B 513 PHE cc_start: 0.7331 (m-10) cc_final: 0.6718 (m-10) REVERT: B 578 ARG cc_start: 0.9467 (mtp180) cc_final: 0.8824 (mtp85) REVERT: B 592 ILE cc_start: 0.9092 (mt) cc_final: 0.8846 (mm) REVERT: B 742 LEU cc_start: 0.8703 (mt) cc_final: 0.8439 (tt) REVERT: C 134 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7576 (pp20) REVERT: C 171 MET cc_start: 0.6922 (mmm) cc_final: 0.6094 (mtp) REVERT: C 212 PHE cc_start: 0.8555 (m-80) cc_final: 0.8068 (m-80) REVERT: C 246 PHE cc_start: 0.7632 (m-80) cc_final: 0.7412 (m-80) REVERT: C 726 ASP cc_start: 0.8389 (t70) cc_final: 0.8099 (t0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.1042 time to fit residues: 59.6897 Evaluate side-chains 333 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN B 121 HIS B 660 HIS C 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.132726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105877 restraints weight = 42615.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.108725 restraints weight = 30386.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.109887 restraints weight = 21167.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.110806 restraints weight = 19479.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.111089 restraints weight = 17914.734| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13795 Z= 0.122 Angle : 0.669 10.193 18529 Z= 0.338 Chirality : 0.045 0.193 2007 Planarity : 0.004 0.054 2364 Dihedral : 4.619 19.376 1813 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 aren not related in a simple way. whole: -1.58 (0.20), residues: 1653 helix: 0.22 (0.19), residues: 739 sheet: -0.31 (0.50), residues: 126 loop : -2.51 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 167 TYR 0.021 0.001 TYR B 692 PHE 0.036 0.001 PHE A 161 TRP 0.023 0.002 TRP C 53 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00266 (13795) covalent geometry : angle 0.66902 (18529) hydrogen bonds : bond 0.04065 ( 564) hydrogen bonds : angle 4.76492 ( 1593) *********************** 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 389 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 28 TYR cc_start: 0.8279 (t80) cc_final: 0.8014 (t80) REVERT: A 116 TYR cc_start: 0.7982 (t80) cc_final: 0.7024 (m-80) REVERT: A 161 PHE cc_start: 0.9237 (m-80) cc_final: 0.8983 (m-80) REVERT: A 208 TYR cc_start: 0.8611 (t80) cc_final: 0.8257 (t80) REVERT: A 269 ASP cc_start: 0.7876 (m-30) cc_final: 0.7395 (t0) REVERT: A 297 MET cc_start: 0.9025 (mpp) cc_final: 0.8737 (mpp) REVERT: A 319 TRP cc_start: 0.8342 (t-100) cc_final: 0.8032 (t-100) REVERT: A 323 LYS cc_start: 0.8312 (mttm) cc_final: 0.8065 (mtpp) REVERT: A 357 TRP cc_start: 0.7800 (t60) cc_final: 0.7415 (t60) REVERT: A 382 PHE cc_start: 0.8280 (t80) cc_final: 0.7872 (t80) REVERT: A 403 TRP cc_start: 0.8847 (m-10) cc_final: 0.8408 (m-10) REVERT: A 406 MET cc_start: 0.8901 (tpt) cc_final: 0.8637 (tpt) REVERT: A 467 TYR cc_start: 0.8062 (p90) cc_final: 0.7739 (p90) REVERT: A 499 THR cc_start: 0.7928 (m) cc_final: 0.7571 (t) REVERT: A 503 PHE cc_start: 0.5419 (m-10) cc_final: 0.4905 (m-10) REVERT: A 559 LYS cc_start: 0.9608 (tppp) cc_final: 0.9356 (mmmt) REVERT: A 560 ASN cc_start: 0.9198 (m110) cc_final: 0.8920 (m110) REVERT: A 606 HIS cc_start: 0.7994 (p-80) cc_final: 0.7381 (p-80) REVERT: A 628 ILE cc_start: 0.9389 (tp) cc_final: 0.9182 (tp) REVERT: A 643 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 645 PHE cc_start: 0.8509 (t80) cc_final: 0.7860 (t80) REVERT: A 649 GLN cc_start: 0.9427 (pt0) cc_final: 0.9180 (pt0) REVERT: A 651 LYS cc_start: 0.9432 (tppt) cc_final: 0.8682 (mttt) REVERT: A 659 ASP cc_start: 0.9201 (t0) cc_final: 0.8865 (t0) REVERT: A 684 ASN cc_start: 0.9453 (t0) cc_final: 0.9184 (t0) REVERT: B 2 GLU cc_start: 0.8445 (tp30) cc_final: 0.8075 (tp30) REVERT: B 19 SER cc_start: 0.9595 (p) cc_final: 0.9022 (p) REVERT: B 25 THR cc_start: 0.8943 (p) cc_final: 0.8652 (p) REVERT: B 41 GLU cc_start: 0.8874 (tt0) cc_final: 0.8406 (tm-30) REVERT: B 45 ARG cc_start: 0.8517 (ttp-170) cc_final: 0.7690 (ttp-170) REVERT: B 49 TYR cc_start: 0.8741 (m-80) cc_final: 0.8348 (m-80) REVERT: B 95 GLU cc_start: 0.8162 (tt0) cc_final: 0.7728 (tm-30) REVERT: B 96 MET cc_start: 0.8372 (mmt) cc_final: 0.7688 (mmt) REVERT: B 121 HIS cc_start: 0.7765 (t70) cc_final: 0.7430 (t-90) REVERT: B 129 ARG cc_start: 0.8745 (ptp90) cc_final: 0.8388 (ptm160) REVERT: B 185 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8426 (pttt) REVERT: B 210 MET cc_start: 0.6543 (pmm) cc_final: 0.5927 (pmm) REVERT: B 248 MET cc_start: 0.8025 (tpp) cc_final: 0.7759 (tpp) REVERT: B 323 MET cc_start: 0.8198 (mmm) cc_final: 0.7771 (mmm) REVERT: B 348 ASN cc_start: 0.9095 (p0) cc_final: 0.8316 (t0) REVERT: B 366 LYS cc_start: 0.7379 (pttp) cc_final: 0.6802 (pttp) REVERT: B 381 LEU cc_start: 0.8291 (mp) cc_final: 0.8020 (mp) REVERT: B 446 ASP cc_start: 0.8329 (p0) cc_final: 0.7788 (p0) REVERT: B 449 VAL cc_start: 0.8752 (t) cc_final: 0.8464 (p) REVERT: B 450 LEU cc_start: 0.8889 (tp) cc_final: 0.8576 (tp) REVERT: B 491 PHE cc_start: 0.7782 (p90) cc_final: 0.7043 (p90) REVERT: B 502 PHE cc_start: 0.8191 (m-80) cc_final: 0.7983 (m-10) REVERT: B 513 PHE cc_start: 0.7361 (m-10) cc_final: 0.6806 (m-10) REVERT: B 544 THR cc_start: 0.7988 (p) cc_final: 0.7745 (p) REVERT: B 578 ARG cc_start: 0.9485 (mtp180) cc_final: 0.8825 (mtp85) REVERT: B 708 MET cc_start: 0.1831 (pmm) cc_final: 0.1614 (pmm) REVERT: C 126 PHE cc_start: 0.8243 (m-10) cc_final: 0.8009 (m-80) REVERT: C 134 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7613 (pp20) REVERT: C 142 PHE cc_start: 0.7948 (m-10) cc_final: 0.7679 (m-10) REVERT: C 171 MET cc_start: 0.6858 (mmm) cc_final: 0.6057 (mtp) REVERT: C 246 PHE cc_start: 0.7797 (m-80) cc_final: 0.7413 (m-80) REVERT: C 726 ASP cc_start: 0.8395 (t70) cc_final: 0.7910 (t70) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.1124 time to fit residues: 63.2299 Evaluate side-chains 331 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 141 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.0970 chunk 152 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN B 660 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102278 restraints weight = 44317.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105487 restraints weight = 29808.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107797 restraints weight = 22001.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.109508 restraints weight = 17311.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.110689 restraints weight = 14365.637| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13795 Z= 0.136 Angle : 0.678 10.148 18529 Z= 0.346 Chirality : 0.045 0.190 2007 Planarity : 0.004 0.052 2364 Dihedral : 4.655 20.136 1813 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.80 % 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 aren not related in a simple way. whole: -1.59 (0.20), residues: 1653 helix: 0.23 (0.19), residues: 744 sheet: -0.37 (0.51), residues: 125 loop : -2.54 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.045 0.002 TYR C 32 PHE 0.030 0.002 PHE A 161 TRP 0.028 0.002 TRP A 386 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00299 (13795) covalent geometry : angle 0.67777 (18529) hydrogen bonds : bond 0.04146 ( 564) hydrogen bonds : angle 4.78398 ( 1593) *********************** 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 379 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 28 TYR cc_start: 0.8293 (t80) cc_final: 0.8028 (t80) REVERT: A 116 TYR cc_start: 0.7972 (t80) cc_final: 0.7008 (m-80) REVERT: A 161 PHE cc_start: 0.9244 (m-80) cc_final: 0.8885 (m-80) REVERT: A 164 ASP cc_start: 0.8620 (t70) cc_final: 0.8126 (t0) REVERT: A 175 MET cc_start: 0.8310 (pmm) cc_final: 0.7984 (pmm) REVERT: A 269 ASP cc_start: 0.7830 (m-30) cc_final: 0.7618 (t0) REVERT: A 297 MET cc_start: 0.9050 (mpp) cc_final: 0.8710 (mpp) REVERT: A 319 TRP cc_start: 0.8265 (t-100) cc_final: 0.7943 (t-100) REVERT: A 357 TRP cc_start: 0.7678 (t60) cc_final: 0.7330 (t60) REVERT: A 382 PHE cc_start: 0.8413 (t80) cc_final: 0.7835 (t80) REVERT: A 403 TRP cc_start: 0.8868 (m-10) cc_final: 0.8378 (m-10) REVERT: A 425 GLU cc_start: 0.8543 (pp20) cc_final: 0.7983 (pp20) REVERT: A 426 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 467 TYR cc_start: 0.7972 (p90) cc_final: 0.7700 (p90) REVERT: A 559 LYS cc_start: 0.9614 (tppp) cc_final: 0.9254 (mmmt) REVERT: A 606 HIS cc_start: 0.7704 (p-80) cc_final: 0.7225 (p-80) REVERT: A 643 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 645 PHE cc_start: 0.8689 (t80) cc_final: 0.7993 (t80) REVERT: A 651 LYS cc_start: 0.9463 (tppt) cc_final: 0.8811 (mttt) REVERT: A 659 ASP cc_start: 0.9219 (t0) cc_final: 0.8851 (t0) REVERT: A 684 ASN cc_start: 0.9468 (t0) cc_final: 0.9213 (t0) REVERT: A 693 ARG cc_start: 0.7431 (mmt180) cc_final: 0.7054 (mmt90) REVERT: B 3 ILE cc_start: 0.7964 (tt) cc_final: 0.7753 (tt) REVERT: B 4 ASN cc_start: 0.8832 (t0) cc_final: 0.8603 (t0) REVERT: B 19 SER cc_start: 0.9607 (p) cc_final: 0.9100 (p) REVERT: B 25 THR cc_start: 0.8977 (p) cc_final: 0.8698 (p) REVERT: B 41 GLU cc_start: 0.8978 (tt0) cc_final: 0.8363 (tm-30) REVERT: B 45 ARG cc_start: 0.8568 (ttp-170) cc_final: 0.7742 (ttp-170) REVERT: B 95 GLU cc_start: 0.8164 (tt0) cc_final: 0.7728 (tm-30) REVERT: B 96 MET cc_start: 0.8228 (mmt) cc_final: 0.7514 (mmt) REVERT: B 132 TYR cc_start: 0.8325 (t80) cc_final: 0.8066 (t80) REVERT: B 140 MET cc_start: 0.8807 (mmm) cc_final: 0.8586 (mmm) REVERT: B 185 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8287 (pptt) REVERT: B 210 MET cc_start: 0.6543 (pmm) cc_final: 0.5854 (pmm) REVERT: B 219 PHE cc_start: 0.8863 (t80) cc_final: 0.8537 (t80) REVERT: B 323 MET cc_start: 0.7900 (mmm) cc_final: 0.7084 (mmm) REVERT: B 348 ASN cc_start: 0.9011 (p0) cc_final: 0.8125 (t0) REVERT: B 366 LYS cc_start: 0.7258 (pttp) cc_final: 0.6709 (pttp) REVERT: B 381 LEU cc_start: 0.8254 (mp) cc_final: 0.7938 (mp) REVERT: B 446 ASP cc_start: 0.8485 (p0) cc_final: 0.7880 (p0) REVERT: B 447 ASP cc_start: 0.7865 (m-30) cc_final: 0.7630 (m-30) REVERT: B 450 LEU cc_start: 0.8811 (tp) cc_final: 0.8570 (tp) REVERT: B 491 PHE cc_start: 0.7857 (p90) cc_final: 0.7405 (p90) REVERT: B 513 PHE cc_start: 0.7086 (m-10) cc_final: 0.6499 (m-10) REVERT: C 7 LEU cc_start: 0.8951 (mm) cc_final: 0.8603 (mm) REVERT: C 10 GLU cc_start: 0.9232 (pt0) cc_final: 0.8669 (pp20) REVERT: C 24 LEU cc_start: 0.9105 (tp) cc_final: 0.8896 (pp) REVERT: C 134 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7972 (mm-30) REVERT: C 140 MET cc_start: 0.6087 (mtt) cc_final: 0.5730 (mtt) REVERT: C 171 MET cc_start: 0.6958 (mmm) cc_final: 0.6127 (mtp) REVERT: C 726 ASP cc_start: 0.8419 (t70) cc_final: 0.7970 (t70) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1082 time to fit residues: 60.0197 Evaluate side-chains 314 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 137 optimal weight: 0.0570 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 560 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.130618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102600 restraints weight = 44852.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105568 restraints weight = 30690.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.107728 restraints weight = 22901.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109234 restraints weight = 18280.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110328 restraints weight = 15391.398| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13795 Z= 0.137 Angle : 0.681 10.206 18529 Z= 0.347 Chirality : 0.046 0.194 2007 Planarity : 0.004 0.049 2364 Dihedral : 4.651 20.632 1813 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.20), residues: 1653 helix: 0.20 (0.19), residues: 748 sheet: -0.57 (0.48), residues: 130 loop : -2.50 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 167 TYR 0.032 0.002 TYR C 32 PHE 0.042 0.002 PHE C 126 TRP 0.032 0.002 TRP C 53 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00303 (13795) covalent geometry : angle 0.68134 (18529) hydrogen bonds : bond 0.04182 ( 564) hydrogen bonds : angle 4.76859 ( 1593) ********************** 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 363 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8309 (t80) cc_final: 0.7983 (t80) REVERT: A 116 TYR cc_start: 0.7959 (t80) cc_final: 0.6996 (m-80) REVERT: A 161 PHE cc_start: 0.9248 (m-80) cc_final: 0.8604 (m-80) REVERT: A 175 MET cc_start: 0.8257 (pmm) cc_final: 0.7983 (pmm) REVERT: A 187 MET cc_start: 0.7739 (pmm) cc_final: 0.7534 (pmm) REVERT: A 208 TYR cc_start: 0.8739 (t80) cc_final: 0.8310 (t80) REVERT: A 269 ASP cc_start: 0.7765 (m-30) cc_final: 0.7205 (t0) REVERT: A 297 MET cc_start: 0.8998 (mpp) cc_final: 0.8750 (mpp) REVERT: A 319 TRP cc_start: 0.8212 (t-100) cc_final: 0.7932 (t-100) REVERT: A 357 TRP cc_start: 0.7728 (t60) cc_final: 0.7392 (t60) REVERT: A 382 PHE cc_start: 0.8499 (t80) cc_final: 0.7881 (t80) REVERT: A 559 LYS cc_start: 0.9623 (tppp) cc_final: 0.8927 (mmmm) REVERT: A 563 PHE cc_start: 0.9239 (m-80) cc_final: 0.8965 (m-80) REVERT: A 606 HIS cc_start: 0.7808 (p-80) cc_final: 0.7579 (p-80) REVERT: A 643 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 645 PHE cc_start: 0.8698 (t80) cc_final: 0.8044 (t80) REVERT: A 649 GLN cc_start: 0.9318 (pt0) cc_final: 0.9107 (pt0) REVERT: A 651 LYS cc_start: 0.9468 (tppt) cc_final: 0.8834 (mttt) REVERT: A 684 ASN cc_start: 0.9440 (t0) cc_final: 0.9171 (t0) REVERT: A 697 LEU cc_start: 0.9410 (tp) cc_final: 0.9204 (tp) REVERT: B 19 SER cc_start: 0.9624 (p) cc_final: 0.9088 (p) REVERT: B 25 THR cc_start: 0.9040 (p) cc_final: 0.8773 (p) REVERT: B 41 GLU cc_start: 0.9094 (tt0) cc_final: 0.8511 (tm-30) REVERT: B 45 ARG cc_start: 0.8604 (ttp-170) cc_final: 0.7731 (ttp-170) REVERT: B 95 GLU cc_start: 0.8106 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 96 MET cc_start: 0.8206 (mmt) cc_final: 0.7510 (mmt) REVERT: B 132 TYR cc_start: 0.8384 (t80) cc_final: 0.8178 (t80) REVERT: B 185 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8624 (mtpp) REVERT: B 219 PHE cc_start: 0.8793 (t80) cc_final: 0.8558 (t80) REVERT: B 248 MET cc_start: 0.8049 (tpp) cc_final: 0.7507 (tpp) REVERT: B 348 ASN cc_start: 0.8987 (p0) cc_final: 0.8167 (t0) REVERT: B 366 LYS cc_start: 0.7267 (pttp) cc_final: 0.6703 (pttp) REVERT: B 378 ARG cc_start: 0.8858 (mmt180) cc_final: 0.8567 (mmt180) REVERT: B 397 MET cc_start: 0.7146 (mmp) cc_final: 0.5396 (tpt) REVERT: B 491 PHE cc_start: 0.7951 (p90) cc_final: 0.7209 (p90) REVERT: B 513 PHE cc_start: 0.7205 (m-10) cc_final: 0.6591 (m-10) REVERT: B 578 ARG cc_start: 0.9479 (mtp180) cc_final: 0.8877 (mtp180) REVERT: C 7 LEU cc_start: 0.8963 (mm) cc_final: 0.8449 (mm) REVERT: C 10 GLU cc_start: 0.9250 (pt0) cc_final: 0.8635 (pp20) REVERT: C 24 LEU cc_start: 0.9134 (tp) cc_final: 0.8875 (pp) REVERT: C 726 ASP cc_start: 0.8396 (t70) cc_final: 0.7928 (t70) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1074 time to fit residues: 56.9225 Evaluate side-chains 310 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 515 HIS A 560 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS C 106 ASN C 744 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095979 restraints weight = 45688.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.099001 restraints weight = 30506.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101070 restraints weight = 22446.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.102641 restraints weight = 17823.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103740 restraints weight = 14901.144| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13795 Z= 0.208 Angle : 0.760 10.755 18529 Z= 0.395 Chirality : 0.048 0.279 2007 Planarity : 0.005 0.050 2364 Dihedral : 5.087 23.368 1813 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.86 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % 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 aren not related in a simple way. whole: -1.90 (0.20), residues: 1653 helix: -0.06 (0.18), residues: 749 sheet: -0.84 (0.46), residues: 130 loop : -2.63 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 45 TYR 0.024 0.002 TYR C 32 PHE 0.050 0.003 PHE C 126 TRP 0.032 0.003 TRP C 38 HIS 0.011 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00445 (13795) covalent geometry : angle 0.76009 (18529) hydrogen bonds : bond 0.04687 ( 564) hydrogen bonds : angle 5.15678 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2326.40 seconds wall clock time: 40 minutes 58.47 seconds (2458.47 seconds total)