Starting phenix.real_space_refine on Thu Jul 31 15:15:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kv5_9577/07_2025/6kv5_9577_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kv5_9577/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kv5_9577/07_2025/6kv5_9577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kv5_9577/07_2025/6kv5_9577.map" model { file = "/net/cci-nas-00/data/ceres_data/6kv5_9577/07_2025/6kv5_9577_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kv5_9577/07_2025/6kv5_9577_neut.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 2} 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, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 8.22, per 1000 atoms: 0.61 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.48 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: 4.31 Time building geometry restraints manager: 3.93 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: 0.410 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.500 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 : 7.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.003 TRP C 38 HIS 0.007 0.002 HIS A 31 PHE 0.023 0.002 PHE A 161 TYR 0.021 0.002 TYR A 289 ARG 0.010 0.001 ARG B 723 Details of bonding type rmsd hydrogen bonds : bond 0.13787 ( 564) hydrogen bonds : angle 10.11991 ( 1593) covalent geometry : bond 0.00374 (13795) covalent geometry : angle 0.82226 (18529) *********************** 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 : 1.489 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 116 TYR cc_start: 0.8492 (t80) cc_final: 0.8062 (m-80) REVERT: A 171 MET cc_start: 0.8263 (mtm) cc_final: 0.7476 (mtm) REVERT: A 173 THR cc_start: 0.8839 (p) cc_final: 0.8329 (p) REVERT: A 208 TYR cc_start: 0.9241 (t80) cc_final: 0.9039 (t80) REVERT: A 228 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8513 (ptmm) REVERT: A 269 ASP cc_start: 0.8050 (m-30) cc_final: 0.7682 (t70) REVERT: A 318 LEU cc_start: 0.9138 (tp) cc_final: 0.8931 (mp) REVERT: A 319 TRP cc_start: 0.8493 (t-100) cc_final: 0.7912 (t-100) REVERT: A 323 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8272 (ptpt) REVERT: A 382 PHE cc_start: 0.8067 (t80) cc_final: 0.7161 (t80) REVERT: A 447 ILE cc_start: 0.9433 (mt) cc_final: 0.9069 (mt) REVERT: A 467 TYR cc_start: 0.8279 (p90) cc_final: 0.7935 (p90) REVERT: A 565 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8288 (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: 0.6878 (p90) REVERT: A 622 ASP cc_start: 0.9010 (m-30) cc_final: 0.8212 (p0) REVERT: A 624 CYS cc_start: 0.9476 (p) cc_final: 0.8995 (p) REVERT: A 628 ILE cc_start: 0.9164 (tp) cc_final: 0.8823 (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: 0.8188 (mm-30) REVERT: A 645 PHE cc_start: 0.8974 (t80) cc_final: 0.8326 (t80) REVERT: A 651 LYS cc_start: 0.9408 (mtpm) cc_final: 0.8947 (mttt) REVERT: A 659 ASP cc_start: 0.8995 (t70) cc_final: 0.8683 (t0) REVERT: A 669 ASN cc_start: 0.8677 (t0) cc_final: 0.8369 (t0) REVERT: A 684 ASN cc_start: 0.9453 (t0) cc_final: 0.9169 (t0) REVERT: B 41 GLU cc_start: 0.8860 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 45 ARG cc_start: 0.8545 (ttp-170) cc_final: 0.8063 (ttp-170) REVERT: B 91 LEU cc_start: 0.9344 (mt) cc_final: 0.8949 (mt) REVERT: B 96 MET cc_start: 0.8209 (ttm) cc_final: 0.7613 (ttm) REVERT: B 132 TYR cc_start: 0.8392 (t80) cc_final: 0.8186 (t80) REVERT: B 248 MET cc_start: 0.8169 (tpp) cc_final: 0.7604 (tpp) REVERT: B 250 ILE cc_start: 0.8786 (mt) cc_final: 0.8397 (mt) REVERT: B 323 MET cc_start: 0.8550 (ttt) cc_final: 0.8316 (ttt) REVERT: B 326 TYR cc_start: 0.8449 (t80) cc_final: 0.8003 (t80) REVERT: B 353 MET cc_start: 0.7687 (mmm) cc_final: 0.7257 (mpp) REVERT: B 390 PHE cc_start: 0.8553 (t80) cc_final: 0.8298 (t80) REVERT: B 403 PHE cc_start: 0.8201 (t80) cc_final: 0.7542 (t80) REVERT: B 416 LEU cc_start: 0.8787 (tp) cc_final: 0.8464 (tp) REVERT: B 423 MET cc_start: 0.7997 (mtp) cc_final: 0.7547 (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: 0.8160 (p90) REVERT: B 513 PHE cc_start: 0.6850 (m-10) cc_final: 0.6600 (m-80) REVERT: B 528 MET cc_start: 0.7311 (mtm) cc_final: 0.6670 (mtm) REVERT: B 581 ILE cc_start: 0.8999 (tp) cc_final: 0.8626 (tp) REVERT: B 692 TYR cc_start: 0.8711 (t80) cc_final: 0.8038 (t80) REVERT: B 702 ASN cc_start: 0.7913 (t0) cc_final: 0.7673 (t0) REVERT: B 710 MET cc_start: 0.8252 (mtp) cc_final: 0.7237 (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: 0.8976 (t) REVERT: C 726 ASP cc_start: 0.8415 (m-30) cc_final: 0.7941 (t70) outliers start: 6 outliers final: 2 residues processed: 586 average time/residue: 0.3255 time to fit residues: 256.1590 Evaluate side-chains 358 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 356 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 0.0970 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.132343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103389 restraints weight = 41041.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.106535 restraints weight = 27843.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.108760 restraints weight = 20575.387| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13795 Z= 0.169 Angle : 0.694 11.223 18529 Z= 0.360 Chirality : 0.044 0.213 2007 Planarity : 0.005 0.054 2364 Dihedral : 5.165 24.552 1813 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.18), residues: 1653 helix: -1.35 (0.17), residues: 748 sheet: -1.35 (0.46), residues: 140 loop : -2.97 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 386 HIS 0.006 0.001 HIS A 31 PHE 0.025 0.002 PHE B 219 TYR 0.018 0.001 TYR A 205 ARG 0.007 0.001 ARG B 748 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 564) hydrogen bonds : angle 5.99388 ( 1593) covalent geometry : bond 0.00363 (13795) covalent geometry : angle 0.69413 (18529) *********************** 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 414 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 1.817 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: 0.8332 (t80) cc_final: 0.7399 (m-80) REVERT: A 228 LYS cc_start: 0.9029 (tmmt) cc_final: 0.8587 (ptmm) REVERT: A 269 ASP cc_start: 0.7791 (m-30) cc_final: 0.7324 (t70) REVERT: A 316 HIS cc_start: 0.8311 (t70) cc_final: 0.8104 (t-90) REVERT: A 319 TRP cc_start: 0.8654 (t-100) cc_final: 0.8151 (t-100) REVERT: A 357 TRP cc_start: 0.7916 (t60) cc_final: 0.7439 (t60) REVERT: A 382 PHE cc_start: 0.7522 (t80) cc_final: 0.6685 (t80) REVERT: A 447 ILE cc_start: 0.9490 (mt) cc_final: 0.9159 (tt) REVERT: A 467 TYR cc_start: 0.8154 (p90) cc_final: 0.7766 (p90) REVERT: A 480 LEU cc_start: 0.8488 (tp) cc_final: 0.8230 (tp) REVERT: A 497 MET cc_start: 0.5879 (mmp) cc_final: 0.5475 (mtt) REVERT: A 503 PHE cc_start: 0.5906 (m-10) cc_final: 0.5293 (m-10) REVERT: A 555 MET cc_start: 0.8154 (mmp) cc_final: 0.7821 (mmp) REVERT: A 559 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9288 (mmmm) REVERT: A 568 ARG cc_start: 0.7550 (mpp-170) cc_final: 0.7057 (mpp-170) REVERT: A 574 MET cc_start: 0.7289 (ttt) cc_final: 0.6481 (ttt) REVERT: A 606 HIS cc_start: 0.7680 (p90) cc_final: 0.7277 (p90) REVERT: A 622 ASP cc_start: 0.8676 (m-30) cc_final: 0.8357 (p0) REVERT: A 631 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8686 (mm-40) REVERT: A 643 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 645 PHE cc_start: 0.8724 (t80) cc_final: 0.7889 (t80) REVERT: A 649 GLN cc_start: 0.9488 (pt0) cc_final: 0.9083 (pt0) REVERT: A 669 ASN cc_start: 0.8680 (t0) cc_final: 0.8319 (t0) REVERT: B 4 ASN cc_start: 0.9152 (t0) cc_final: 0.8917 (t0) REVERT: B 14 ILE cc_start: 0.9215 (mm) cc_final: 0.8946 (mm) REVERT: B 25 THR cc_start: 0.8973 (p) cc_final: 0.8692 (p) REVERT: B 41 GLU cc_start: 0.8919 (tt0) cc_final: 0.8393 (tm-30) REVERT: B 45 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8205 (ttp-170) REVERT: B 91 LEU cc_start: 0.9243 (mt) cc_final: 0.8793 (mt) REVERT: B 140 MET cc_start: 0.8599 (mmm) cc_final: 0.8144 (tpp) REVERT: B 226 ILE cc_start: 0.7940 (mp) cc_final: 0.7554 (mp) REVERT: B 248 MET cc_start: 0.8318 (tpp) cc_final: 0.7751 (tpp) REVERT: B 326 TYR cc_start: 0.8561 (t80) cc_final: 0.8349 (t80) REVERT: B 346 PHE cc_start: 0.8599 (m-10) cc_final: 0.8255 (m-10) REVERT: B 348 ASN cc_start: 0.9095 (p0) cc_final: 0.8257 (t0) REVERT: B 390 PHE cc_start: 0.8954 (t80) cc_final: 0.8556 (t80) REVERT: B 403 PHE cc_start: 0.8128 (t80) cc_final: 0.7879 (t80) REVERT: B 416 LEU cc_start: 0.8812 (tp) cc_final: 0.8529 (tp) REVERT: B 426 ASN cc_start: 0.9243 (m-40) cc_final: 0.8573 (m110) REVERT: B 446 ASP cc_start: 0.8377 (p0) cc_final: 0.8127 (p0) REVERT: B 449 VAL cc_start: 0.8980 (t) cc_final: 0.8687 (p) REVERT: B 450 LEU cc_start: 0.8956 (tp) cc_final: 0.8699 (tp) REVERT: B 494 THR cc_start: 0.7561 (p) cc_final: 0.6803 (p) REVERT: B 513 PHE cc_start: 0.7266 (m-10) cc_final: 0.6756 (m-10) REVERT: B 544 THR cc_start: 0.8619 (p) cc_final: 0.7597 (p) REVERT: B 611 ILE cc_start: 0.9576 (mt) cc_final: 0.9280 (tt) REVERT: B 665 ARG cc_start: 0.7578 (tpt90) cc_final: 0.6858 (tpp80) REVERT: B 691 MET cc_start: 0.8344 (mmm) cc_final: 0.7956 (mmm) REVERT: B 702 ASN cc_start: 0.7736 (t0) cc_final: 0.7283 (m-40) REVERT: B 714 ILE cc_start: 0.9383 (mt) cc_final: 0.9046 (mt) REVERT: C 10 GLU cc_start: 0.9224 (pt0) cc_final: 0.8527 (pp20) REVERT: C 81 ASP cc_start: 0.7772 (t0) cc_final: 0.7503 (t0) REVERT: C 148 GLN cc_start: 0.8493 (pm20) cc_final: 0.8279 (pm20) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.2929 time to fit residues: 168.7077 Evaluate side-chains 318 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 106 ASN C 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.129733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101998 restraints weight = 41898.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104814 restraints weight = 29413.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.107074 restraints weight = 20311.928| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13795 Z= 0.165 Angle : 0.672 11.380 18529 Z= 0.349 Chirality : 0.044 0.170 2007 Planarity : 0.005 0.076 2364 Dihedral : 4.978 19.600 1813 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.19), residues: 1653 helix: -0.66 (0.18), residues: 752 sheet: -1.17 (0.48), residues: 128 loop : -2.72 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 386 HIS 0.006 0.001 HIS A 31 PHE 0.021 0.002 PHE C 212 TYR 0.019 0.002 TYR B 560 ARG 0.011 0.001 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 564) hydrogen bonds : angle 5.44695 ( 1593) covalent geometry : bond 0.00355 (13795) covalent geometry : angle 0.67168 (18529) *********************** 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 397 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 1.510 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: A 116 TYR cc_start: 0.8285 (t80) cc_final: 0.7295 (m-80) REVERT: A 196 MET cc_start: 0.8723 (ppp) cc_final: 0.8266 (ptp) REVERT: A 208 TYR cc_start: 0.8833 (t80) cc_final: 0.8439 (t80) REVERT: A 222 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8001 (pm20) REVERT: A 231 ASP cc_start: 0.7748 (t0) cc_final: 0.7366 (t0) REVERT: A 269 ASP cc_start: 0.7962 (m-30) cc_final: 0.7404 (t0) REVERT: A 323 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7554 (mtpp) REVERT: A 357 TRP cc_start: 0.7988 (t60) cc_final: 0.7500 (t60) REVERT: A 364 GLU cc_start: 0.8671 (mp0) cc_final: 0.8398 (mp0) REVERT: A 382 PHE cc_start: 0.7738 (t80) cc_final: 0.7521 (t80) REVERT: A 403 TRP cc_start: 0.8715 (m-90) cc_final: 0.7934 (m-90) REVERT: A 426 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8209 (mt-10) REVERT: A 428 GLU cc_start: 0.8537 (tp30) cc_final: 0.8268 (tp30) REVERT: A 440 MET cc_start: 0.8683 (mmm) cc_final: 0.8477 (mmm) REVERT: A 467 TYR cc_start: 0.8159 (p90) cc_final: 0.7815 (p90) REVERT: A 499 THR cc_start: 0.7768 (m) cc_final: 0.7391 (t) REVERT: A 503 PHE cc_start: 0.5279 (m-10) cc_final: 0.5000 (m-10) REVERT: A 574 MET cc_start: 0.7490 (ttt) cc_final: 0.6411 (ttt) REVERT: A 606 HIS cc_start: 0.7877 (p90) cc_final: 0.5960 (p-80) REVERT: A 622 ASP cc_start: 0.8959 (m-30) cc_final: 0.8350 (p0) REVERT: A 643 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 645 PHE cc_start: 0.8680 (t80) cc_final: 0.8071 (t80) REVERT: A 649 GLN cc_start: 0.9444 (pt0) cc_final: 0.9163 (pt0) REVERT: A 659 ASP cc_start: 0.8961 (t70) cc_final: 0.8623 (t0) REVERT: A 669 ASN cc_start: 0.8595 (t0) cc_final: 0.8275 (t0) REVERT: A 684 ASN cc_start: 0.9539 (t0) cc_final: 0.9320 (t0) REVERT: B 2 GLU cc_start: 0.8031 (tt0) cc_final: 0.7766 (tt0) REVERT: B 4 ASN cc_start: 0.9207 (t0) cc_final: 0.8925 (t0) REVERT: B 41 GLU cc_start: 0.8922 (tt0) cc_final: 0.8505 (tm-30) REVERT: B 45 ARG cc_start: 0.8668 (ttp-170) cc_final: 0.8352 (ttp-170) REVERT: B 129 ARG cc_start: 0.8917 (ptp-170) cc_final: 0.8708 (ptm160) REVERT: B 132 TYR cc_start: 0.8109 (t80) cc_final: 0.7896 (t80) REVERT: B 185 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8425 (pttp) REVERT: B 210 MET cc_start: 0.6534 (pmm) cc_final: 0.5616 (pmm) REVERT: B 248 MET cc_start: 0.8322 (tpp) cc_final: 0.7813 (tpp) REVERT: B 335 MET cc_start: 0.8720 (mmm) cc_final: 0.8377 (ptm) REVERT: B 346 PHE cc_start: 0.8597 (m-10) cc_final: 0.8258 (m-10) REVERT: B 348 ASN cc_start: 0.9171 (p0) cc_final: 0.8268 (t0) REVERT: B 390 PHE cc_start: 0.8937 (t80) cc_final: 0.8596 (t80) REVERT: B 426 ASN cc_start: 0.9237 (m-40) cc_final: 0.8604 (m110) REVERT: B 455 ARG cc_start: 0.7995 (mmt180) cc_final: 0.7773 (mmm-85) REVERT: B 462 MET cc_start: 0.9004 (tpp) cc_final: 0.8622 (tpp) REVERT: B 494 THR cc_start: 0.7680 (p) cc_final: 0.7448 (t) REVERT: B 502 PHE cc_start: 0.8594 (m-80) cc_final: 0.8123 (m-10) REVERT: B 513 PHE cc_start: 0.7103 (m-10) cc_final: 0.6678 (m-10) REVERT: B 544 THR cc_start: 0.8626 (p) cc_final: 0.7723 (p) REVERT: B 665 ARG cc_start: 0.7790 (tpt90) cc_final: 0.7103 (tpp80) REVERT: B 702 ASN cc_start: 0.7781 (t0) cc_final: 0.7356 (m110) REVERT: B 708 MET cc_start: 0.4517 (pmm) cc_final: 0.3888 (ptt) REVERT: B 710 MET cc_start: 0.7751 (mtp) cc_final: 0.7462 (mtp) REVERT: B 736 TYR cc_start: 0.9091 (t80) cc_final: 0.8783 (t80) REVERT: C 81 ASP cc_start: 0.7930 (t0) cc_final: 0.7653 (t0) REVERT: C 126 PHE cc_start: 0.8232 (m-10) cc_final: 0.8004 (m-80) REVERT: C 134 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7309 (pp20) REVERT: C 246 PHE cc_start: 0.7718 (m-80) cc_final: 0.7502 (m-80) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.2689 time to fit residues: 150.1959 Evaluate side-chains 322 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 41 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.129446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102283 restraints weight = 42676.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104825 restraints weight = 30343.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.106948 restraints weight = 21051.279| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13795 Z= 0.145 Angle : 0.660 11.010 18529 Z= 0.338 Chirality : 0.044 0.234 2007 Planarity : 0.005 0.076 2364 Dihedral : 4.895 19.434 1813 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1653 helix: -0.37 (0.18), residues: 742 sheet: -1.07 (0.47), residues: 128 loop : -2.66 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 403 HIS 0.005 0.001 HIS A 263 PHE 0.028 0.002 PHE A 158 TYR 0.013 0.001 TYR B 326 ARG 0.005 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 564) hydrogen bonds : angle 5.17725 ( 1593) covalent geometry : bond 0.00316 (13795) covalent geometry : angle 0.65960 (18529) *********************** 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 401 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 1.676 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: 0.8265 (t80) cc_final: 0.7327 (m-80) REVERT: A 196 MET cc_start: 0.8720 (ppp) cc_final: 0.8356 (ptp) REVERT: A 208 TYR cc_start: 0.8709 (t80) cc_final: 0.8318 (t80) REVERT: A 222 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8201 (pm20) REVERT: A 231 ASP cc_start: 0.7875 (t0) cc_final: 0.7592 (t0) REVERT: A 242 HIS cc_start: 0.7447 (m-70) cc_final: 0.7106 (m-70) REVERT: A 269 ASP cc_start: 0.7995 (m-30) cc_final: 0.7173 (t0) REVERT: A 323 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7578 (mtpp) REVERT: A 357 TRP cc_start: 0.8007 (t60) cc_final: 0.7484 (t60) REVERT: A 382 PHE cc_start: 0.8029 (t80) cc_final: 0.7819 (t80) REVERT: A 403 TRP cc_start: 0.8869 (m-90) cc_final: 0.8011 (m-90) REVERT: A 406 MET cc_start: 0.9174 (tpt) cc_final: 0.8594 (tpt) REVERT: A 425 GLU cc_start: 0.8149 (pp20) cc_final: 0.7881 (pp20) REVERT: A 426 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8447 (mt-10) REVERT: A 442 LYS cc_start: 0.9297 (ptmm) cc_final: 0.9047 (pttt) REVERT: A 467 TYR cc_start: 0.8191 (p90) cc_final: 0.7804 (p90) REVERT: A 499 THR cc_start: 0.7908 (m) cc_final: 0.7549 (t) REVERT: A 503 PHE cc_start: 0.5120 (m-10) cc_final: 0.4650 (m-10) REVERT: A 562 TRP cc_start: 0.8381 (m100) cc_final: 0.7782 (m100) REVERT: A 574 MET cc_start: 0.7447 (ttt) cc_final: 0.6809 (ttt) REVERT: A 606 HIS cc_start: 0.7993 (p90) cc_final: 0.7791 (p-80) REVERT: A 622 ASP cc_start: 0.8975 (m-30) cc_final: 0.8411 (p0) REVERT: A 643 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 645 PHE cc_start: 0.8693 (t80) cc_final: 0.8164 (t80) REVERT: A 649 GLN cc_start: 0.9397 (pt0) cc_final: 0.9196 (pt0) REVERT: A 651 LYS cc_start: 0.9470 (tppt) cc_final: 0.8961 (mttt) REVERT: A 659 ASP cc_start: 0.8871 (t70) cc_final: 0.8664 (t0) REVERT: A 669 ASN cc_start: 0.8560 (t0) cc_final: 0.8176 (t0) REVERT: A 684 ASN cc_start: 0.9514 (t0) cc_final: 0.9298 (t0) REVERT: B 4 ASN cc_start: 0.9268 (t0) cc_final: 0.8898 (t0) REVERT: B 25 THR cc_start: 0.8749 (p) cc_final: 0.8507 (p) REVERT: B 41 GLU cc_start: 0.8870 (tt0) cc_final: 0.8405 (tm-30) REVERT: B 45 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.8301 (ttp-170) REVERT: B 86 ASP cc_start: 0.8715 (t0) cc_final: 0.8499 (t0) REVERT: B 96 MET cc_start: 0.8422 (mmt) cc_final: 0.8189 (mmt) REVERT: B 129 ARG cc_start: 0.8850 (ptp-170) cc_final: 0.8609 (ptm160) REVERT: B 132 TYR cc_start: 0.8129 (t80) cc_final: 0.7842 (t80) REVERT: B 185 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8449 (pttp) REVERT: B 210 MET cc_start: 0.6630 (pmm) cc_final: 0.6050 (pmm) REVERT: B 240 ARG cc_start: 0.6132 (mtm110) cc_final: 0.5373 (ttt-90) REVERT: B 248 MET cc_start: 0.8354 (tpp) cc_final: 0.7935 (tpp) REVERT: B 335 MET cc_start: 0.8616 (mmm) cc_final: 0.8277 (ptm) REVERT: B 348 ASN cc_start: 0.9161 (p0) cc_final: 0.8217 (t0) REVERT: B 423 MET cc_start: 0.8506 (mtp) cc_final: 0.7626 (mtt) REVERT: B 425 LEU cc_start: 0.9356 (tp) cc_final: 0.9143 (tt) REVERT: B 426 ASN cc_start: 0.9347 (m-40) cc_final: 0.8776 (m110) REVERT: B 462 MET cc_start: 0.8856 (tpp) cc_final: 0.8542 (tpp) REVERT: B 494 THR cc_start: 0.7443 (p) cc_final: 0.7175 (t) REVERT: B 502 PHE cc_start: 0.8552 (m-80) cc_final: 0.8248 (m-10) REVERT: B 513 PHE cc_start: 0.7408 (m-10) cc_final: 0.6860 (m-10) REVERT: B 544 THR cc_start: 0.8628 (p) cc_final: 0.7756 (p) REVERT: B 665 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7091 (tpp80) REVERT: B 692 TYR cc_start: 0.8496 (t80) cc_final: 0.8265 (t80) REVERT: B 708 MET cc_start: 0.4115 (pmm) cc_final: 0.3881 (ptt) REVERT: C 126 PHE cc_start: 0.8198 (m-10) cc_final: 0.7977 (m-80) REVERT: C 134 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7416 (pp20) REVERT: C 246 PHE cc_start: 0.7750 (m-80) cc_final: 0.7505 (m-80) REVERT: C 726 ASP cc_start: 0.8390 (t70) cc_final: 0.8091 (t0) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.2838 time to fit residues: 160.4765 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 : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 242 HIS ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** 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 = 0.4068 r_free = 0.4068 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102891 restraints weight = 43479.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.105970 restraints weight = 29343.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107786 restraints weight = 21626.336| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13795 Z= 0.131 Angle : 0.656 10.338 18529 Z= 0.334 Chirality : 0.044 0.262 2007 Planarity : 0.005 0.071 2364 Dihedral : 4.866 18.959 1813 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 0.07 % Allowed : 1.56 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1653 helix: 0.01 (0.18), residues: 740 sheet: -1.05 (0.48), residues: 129 loop : -2.68 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 386 HIS 0.004 0.001 HIS A 263 PHE 0.021 0.002 PHE C 142 TYR 0.011 0.001 TYR A 634 ARG 0.003 0.000 ARG A 568 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 564) hydrogen bonds : angle 4.93846 ( 1593) covalent geometry : bond 0.00294 (13795) covalent geometry : angle 0.65598 (18529) *********************** 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 397 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 1.500 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: 0.8297 (t80) cc_final: 0.8073 (t80) REVERT: A 116 TYR cc_start: 0.8276 (t80) cc_final: 0.7339 (m-80) REVERT: A 164 ASP cc_start: 0.8548 (t0) cc_final: 0.7950 (t0) REVERT: A 187 MET cc_start: 0.7080 (mtt) cc_final: 0.6615 (mpp) REVERT: A 208 TYR cc_start: 0.8726 (t80) cc_final: 0.8324 (t80) REVERT: A 226 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8828 (tp30) REVERT: A 269 ASP cc_start: 0.7756 (m-30) cc_final: 0.7283 (t70) REVERT: A 316 HIS cc_start: 0.8297 (t70) cc_final: 0.8038 (t-170) REVERT: A 357 TRP cc_start: 0.7847 (t60) cc_final: 0.7404 (t60) REVERT: A 382 PHE cc_start: 0.8143 (t80) cc_final: 0.7765 (t80) REVERT: A 403 TRP cc_start: 0.8874 (m-90) cc_final: 0.7918 (m-90) REVERT: A 406 MET cc_start: 0.8835 (tpt) cc_final: 0.8498 (tpt) REVERT: A 413 LYS cc_start: 0.8656 (mppt) cc_final: 0.8152 (mtmm) REVERT: A 426 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 467 TYR cc_start: 0.8180 (p90) cc_final: 0.7805 (p90) REVERT: A 499 THR cc_start: 0.7969 (m) cc_final: 0.7600 (t) REVERT: A 503 PHE cc_start: 0.5007 (m-10) cc_final: 0.4638 (m-10) REVERT: A 559 LYS cc_start: 0.9150 (tptp) cc_final: 0.8754 (tptp) REVERT: A 583 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8746 (pttm) REVERT: A 622 ASP cc_start: 0.8916 (m-30) cc_final: 0.8259 (p0) REVERT: A 624 CYS cc_start: 0.9247 (p) cc_final: 0.8990 (p) REVERT: A 643 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 645 PHE cc_start: 0.8661 (t80) cc_final: 0.8081 (t80) REVERT: A 651 LYS cc_start: 0.9501 (tppt) cc_final: 0.8966 (mttt) REVERT: A 659 ASP cc_start: 0.8856 (t70) cc_final: 0.8616 (t0) REVERT: A 669 ASN cc_start: 0.8535 (t0) cc_final: 0.8215 (t0) REVERT: A 684 ASN cc_start: 0.9488 (t0) cc_final: 0.9261 (t0) REVERT: A 697 LEU cc_start: 0.9443 (tp) cc_final: 0.9133 (tp) REVERT: B 4 ASN cc_start: 0.9226 (t0) cc_final: 0.8814 (t0) REVERT: B 25 THR cc_start: 0.8734 (p) cc_final: 0.8425 (p) REVERT: B 41 GLU cc_start: 0.8831 (tt0) cc_final: 0.8371 (tm-30) REVERT: B 45 ARG cc_start: 0.8581 (ttp-170) cc_final: 0.7182 (ttp-170) REVERT: B 49 TYR cc_start: 0.8838 (m-10) cc_final: 0.8616 (m-80) REVERT: B 96 MET cc_start: 0.8411 (mmt) cc_final: 0.8203 (mmt) REVERT: B 129 ARG cc_start: 0.8794 (ptp-170) cc_final: 0.8563 (ptm160) REVERT: B 172 ILE cc_start: 0.9667 (mt) cc_final: 0.9426 (mm) REVERT: B 185 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8247 (pttp) REVERT: B 210 MET cc_start: 0.6556 (pmm) cc_final: 0.6079 (pmm) REVERT: B 240 ARG cc_start: 0.6127 (mtm110) cc_final: 0.5695 (ttt-90) REVERT: B 248 MET cc_start: 0.8376 (tpp) cc_final: 0.7951 (tpp) REVERT: B 335 MET cc_start: 0.8273 (mmm) cc_final: 0.7974 (ptm) REVERT: B 348 ASN cc_start: 0.9203 (p0) cc_final: 0.8196 (t0) REVERT: B 425 LEU cc_start: 0.9366 (tp) cc_final: 0.9132 (tt) REVERT: B 426 ASN cc_start: 0.9237 (m-40) cc_final: 0.8724 (m110) REVERT: B 462 MET cc_start: 0.8796 (tpp) cc_final: 0.8488 (tpp) REVERT: B 491 PHE cc_start: 0.8205 (p90) cc_final: 0.8002 (p90) REVERT: B 494 THR cc_start: 0.7656 (p) cc_final: 0.7444 (t) REVERT: B 513 PHE cc_start: 0.7230 (m-10) cc_final: 0.6627 (m-10) REVERT: B 518 MET cc_start: 0.7132 (mmp) cc_final: 0.6826 (mmm) REVERT: B 544 THR cc_start: 0.8623 (p) cc_final: 0.7996 (p) REVERT: B 665 ARG cc_start: 0.7710 (tpt90) cc_final: 0.7134 (tpp-160) REVERT: B 691 MET cc_start: 0.8450 (mtp) cc_final: 0.8177 (mtp) REVERT: B 708 MET cc_start: 0.4135 (pmm) cc_final: 0.3624 (ptt) REVERT: B 710 MET cc_start: 0.7756 (mtp) cc_final: 0.7467 (mtp) REVERT: C 7 LEU cc_start: 0.8799 (mm) cc_final: 0.8391 (mm) REVERT: C 10 GLU cc_start: 0.9319 (pt0) cc_final: 0.8820 (pp20) REVERT: C 32 TYR cc_start: 0.7865 (t80) cc_final: 0.7587 (t80) REVERT: C 52 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.8056 (mmt180) REVERT: C 81 ASP cc_start: 0.8280 (t0) cc_final: 0.8041 (t0) REVERT: C 134 GLU cc_start: 0.8328 (tp30) cc_final: 0.7875 (pp20) REVERT: C 171 MET cc_start: 0.6312 (mmm) cc_final: 0.6087 (mmt) REVERT: C 726 ASP cc_start: 0.8455 (t70) cc_final: 0.8124 (t0) outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 0.3015 time to fit residues: 172.0762 Evaluate side-chains 318 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** 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 = 0.4082 r_free = 0.4082 target = 0.131473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103434 restraints weight = 42842.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106457 restraints weight = 28975.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108615 restraints weight = 21473.572| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13795 Z= 0.130 Angle : 0.665 10.240 18529 Z= 0.341 Chirality : 0.044 0.185 2007 Planarity : 0.005 0.062 2364 Dihedral : 4.870 21.243 1813 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.20), residues: 1653 helix: 0.03 (0.19), residues: 740 sheet: -0.83 (0.48), residues: 125 loop : -2.66 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 386 HIS 0.004 0.001 HIS A 263 PHE 0.051 0.002 PHE C 142 TYR 0.010 0.001 TYR B 326 ARG 0.011 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 564) hydrogen bonds : angle 4.86009 ( 1593) covalent geometry : bond 0.00294 (13795) covalent geometry : angle 0.66468 (18529) *********************** 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 386 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 1.637 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: A 28 TYR cc_start: 0.8284 (t80) cc_final: 0.8056 (t80) REVERT: A 116 TYR cc_start: 0.8385 (t80) cc_final: 0.7443 (m-80) REVERT: A 208 TYR cc_start: 0.8611 (t80) cc_final: 0.8242 (t80) REVERT: A 226 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8769 (tp30) REVERT: A 269 ASP cc_start: 0.7648 (m-30) cc_final: 0.7282 (t0) REVERT: A 357 TRP cc_start: 0.7740 (t60) cc_final: 0.7395 (t60) REVERT: A 382 PHE cc_start: 0.8101 (t80) cc_final: 0.7683 (t80) REVERT: A 403 TRP cc_start: 0.8798 (m-90) cc_final: 0.7816 (m-90) REVERT: A 406 MET cc_start: 0.8900 (tpt) cc_final: 0.8440 (tpt) REVERT: A 413 LYS cc_start: 0.8530 (mppt) cc_final: 0.8084 (mtmm) REVERT: A 425 GLU cc_start: 0.8629 (pp20) cc_final: 0.7956 (pp20) REVERT: A 426 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8237 (mm-30) REVERT: A 467 TYR cc_start: 0.8030 (p90) cc_final: 0.7749 (p90) REVERT: A 499 THR cc_start: 0.7729 (m) cc_final: 0.7342 (t) REVERT: A 503 PHE cc_start: 0.4828 (m-10) cc_final: 0.4418 (m-10) REVERT: A 551 ARG cc_start: 0.5944 (ttt180) cc_final: 0.5319 (ttp80) REVERT: A 622 ASP cc_start: 0.8996 (m-30) cc_final: 0.8343 (p0) REVERT: A 624 CYS cc_start: 0.9037 (p) cc_final: 0.8747 (p) REVERT: A 628 ILE cc_start: 0.9502 (tp) cc_final: 0.9274 (tp) REVERT: A 643 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8174 (mm-30) REVERT: A 645 PHE cc_start: 0.8685 (t80) cc_final: 0.8014 (t80) REVERT: A 649 GLN cc_start: 0.9382 (pt0) cc_final: 0.9085 (pt0) REVERT: A 651 LYS cc_start: 0.9436 (tppt) cc_final: 0.8939 (mttt) REVERT: A 669 ASN cc_start: 0.8498 (t0) cc_final: 0.8227 (t0) REVERT: A 684 ASN cc_start: 0.9470 (t0) cc_final: 0.9221 (t0) REVERT: A 697 LEU cc_start: 0.9356 (tp) cc_final: 0.9146 (tp) REVERT: B 4 ASN cc_start: 0.9266 (t0) cc_final: 0.8822 (t0) REVERT: B 41 GLU cc_start: 0.8821 (tt0) cc_final: 0.8347 (tm-30) REVERT: B 45 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.7163 (ttp-170) REVERT: B 49 TYR cc_start: 0.8879 (m-10) cc_final: 0.8666 (m-80) REVERT: B 95 GLU cc_start: 0.8208 (tt0) cc_final: 0.7741 (tm-30) REVERT: B 96 MET cc_start: 0.8468 (mmt) cc_final: 0.7682 (mmt) REVERT: B 129 ARG cc_start: 0.8783 (ptp-170) cc_final: 0.8558 (ptm160) REVERT: B 172 ILE cc_start: 0.9675 (mt) cc_final: 0.9435 (mm) REVERT: B 175 MET cc_start: 0.9421 (ptp) cc_final: 0.9213 (ptm) REVERT: B 185 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8233 (pttp) REVERT: B 210 MET cc_start: 0.6536 (pmm) cc_final: 0.6121 (pmm) REVERT: B 248 MET cc_start: 0.7831 (tpp) cc_final: 0.7521 (tpp) REVERT: B 335 MET cc_start: 0.8561 (mmm) cc_final: 0.8214 (ptm) REVERT: B 348 ASN cc_start: 0.9110 (p0) cc_final: 0.8188 (t0) REVERT: B 397 MET cc_start: 0.7487 (mmp) cc_final: 0.5668 (tpt) REVERT: B 425 LEU cc_start: 0.9341 (tp) cc_final: 0.9123 (tt) REVERT: B 426 ASN cc_start: 0.9230 (m-40) cc_final: 0.8760 (m110) REVERT: B 462 MET cc_start: 0.8688 (tpp) cc_final: 0.8387 (tpp) REVERT: B 491 PHE cc_start: 0.7998 (p90) cc_final: 0.7582 (p90) REVERT: B 513 PHE cc_start: 0.7095 (m-10) cc_final: 0.6781 (m-80) REVERT: B 608 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.8087 (Cg_endo) REVERT: B 665 ARG cc_start: 0.7677 (tpt90) cc_final: 0.6905 (tpp80) REVERT: B 691 MET cc_start: 0.8444 (mtp) cc_final: 0.8190 (mtp) REVERT: B 692 TYR cc_start: 0.8114 (t80) cc_final: 0.7690 (t80) REVERT: B 708 MET cc_start: 0.3663 (pmm) cc_final: 0.3235 (ptt) REVERT: C 7 LEU cc_start: 0.8800 (mm) cc_final: 0.8440 (mm) REVERT: C 10 GLU cc_start: 0.9308 (pt0) cc_final: 0.8806 (pp20) REVERT: C 32 TYR cc_start: 0.7794 (t80) cc_final: 0.7441 (t80) REVERT: C 81 ASP cc_start: 0.8221 (t0) cc_final: 0.7887 (t0) REVERT: C 127 MET cc_start: 0.8385 (mmm) cc_final: 0.7996 (mmm) REVERT: C 134 GLU cc_start: 0.8264 (tp30) cc_final: 0.7863 (pp20) REVERT: C 171 MET cc_start: 0.6474 (mmm) cc_final: 0.5644 (mtp) REVERT: C 726 ASP cc_start: 0.8436 (t70) cc_final: 0.8147 (t0) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.2685 time to fit residues: 147.1416 Evaluate side-chains 317 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 123 optimal weight: 0.0370 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 600 ASN B 660 HIS C 744 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.125132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097813 restraints weight = 43293.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100675 restraints weight = 29334.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102692 restraints weight = 21860.533| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13795 Z= 0.182 Angle : 0.699 12.137 18529 Z= 0.362 Chirality : 0.045 0.184 2007 Planarity : 0.005 0.055 2364 Dihedral : 5.072 21.401 1813 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1653 helix: 0.05 (0.19), residues: 745 sheet: -1.06 (0.46), residues: 130 loop : -2.67 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 386 HIS 0.010 0.002 HIS A 263 PHE 0.038 0.002 PHE A 161 TYR 0.015 0.002 TYR A 633 ARG 0.008 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 564) hydrogen bonds : angle 5.03719 ( 1593) covalent geometry : bond 0.00392 (13795) covalent geometry : angle 0.69909 (18529) *********************** 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 377 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.530 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: A 116 TYR cc_start: 0.8313 (t80) cc_final: 0.7315 (m-80) REVERT: A 161 PHE cc_start: 0.9279 (m-80) cc_final: 0.8874 (m-80) REVERT: A 165 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9175 (mm-30) REVERT: A 208 TYR cc_start: 0.8798 (t80) cc_final: 0.8379 (t80) REVERT: A 269 ASP cc_start: 0.7960 (m-30) cc_final: 0.7303 (t0) REVERT: A 357 TRP cc_start: 0.7640 (t60) cc_final: 0.7172 (t60) REVERT: A 382 PHE cc_start: 0.8581 (t80) cc_final: 0.8079 (t80) REVERT: A 406 MET cc_start: 0.8940 (tpt) cc_final: 0.8445 (tpt) REVERT: A 425 GLU cc_start: 0.8772 (pp20) cc_final: 0.8402 (pp20) REVERT: A 426 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8517 (mt-10) REVERT: A 467 TYR cc_start: 0.8202 (p90) cc_final: 0.7913 (p90) REVERT: A 503 PHE cc_start: 0.5306 (m-10) cc_final: 0.4982 (m-10) REVERT: A 574 MET cc_start: 0.7359 (ttt) cc_final: 0.7144 (ttt) REVERT: A 624 CYS cc_start: 0.9068 (p) cc_final: 0.8853 (p) REVERT: A 628 ILE cc_start: 0.9476 (tp) cc_final: 0.9262 (tp) REVERT: A 643 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 645 PHE cc_start: 0.8653 (t80) cc_final: 0.8032 (t80) REVERT: A 649 GLN cc_start: 0.9497 (pt0) cc_final: 0.9142 (pt0) REVERT: A 651 LYS cc_start: 0.9408 (tppt) cc_final: 0.8608 (mttt) REVERT: A 669 ASN cc_start: 0.8442 (t0) cc_final: 0.8178 (t0) REVERT: A 684 ASN cc_start: 0.9505 (t0) cc_final: 0.9231 (t0) REVERT: B 10 LEU cc_start: 0.9014 (tt) cc_final: 0.8798 (mm) REVERT: B 25 THR cc_start: 0.8936 (p) cc_final: 0.8647 (p) REVERT: B 40 MET cc_start: 0.8699 (ptm) cc_final: 0.8491 (ptm) REVERT: B 41 GLU cc_start: 0.8995 (tt0) cc_final: 0.8463 (tm-30) REVERT: B 45 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8254 (ttm170) REVERT: B 90 MET cc_start: 0.8627 (ppp) cc_final: 0.8411 (ppp) REVERT: B 96 MET cc_start: 0.8418 (mmt) cc_final: 0.8141 (mmt) REVERT: B 129 ARG cc_start: 0.8872 (ptp-170) cc_final: 0.8607 (ptm160) REVERT: B 185 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8360 (pttt) REVERT: B 210 MET cc_start: 0.6549 (pmm) cc_final: 0.5870 (pmm) REVERT: B 248 MET cc_start: 0.7975 (tpp) cc_final: 0.7660 (tpp) REVERT: B 348 ASN cc_start: 0.9177 (p0) cc_final: 0.8186 (t0) REVERT: B 366 LYS cc_start: 0.7285 (pttm) cc_final: 0.6786 (pttp) REVERT: B 378 ARG cc_start: 0.8855 (mmt180) cc_final: 0.8523 (mmt180) REVERT: B 397 MET cc_start: 0.7374 (mmp) cc_final: 0.5927 (tpt) REVERT: B 425 LEU cc_start: 0.9368 (tp) cc_final: 0.9091 (tt) REVERT: B 426 ASN cc_start: 0.9262 (m-40) cc_final: 0.8887 (m110) REVERT: B 491 PHE cc_start: 0.8231 (p90) cc_final: 0.7791 (p90) REVERT: B 544 THR cc_start: 0.8863 (p) cc_final: 0.8155 (p) REVERT: B 665 ARG cc_start: 0.7827 (tpt90) cc_final: 0.7076 (tpp80) REVERT: B 691 MET cc_start: 0.8535 (mtp) cc_final: 0.8292 (mtp) REVERT: B 710 MET cc_start: 0.7579 (mtp) cc_final: 0.7270 (mtp) REVERT: C 10 GLU cc_start: 0.9317 (pt0) cc_final: 0.8755 (pp20) REVERT: C 59 PHE cc_start: 0.7749 (m-10) cc_final: 0.7026 (m-80) REVERT: C 134 GLU cc_start: 0.8470 (tp30) cc_final: 0.8038 (pp20) REVERT: C 171 MET cc_start: 0.6592 (mmm) cc_final: 0.6245 (mmt) REVERT: C 713 CYS cc_start: 0.4760 (p) cc_final: 0.4393 (m) REVERT: C 726 ASP cc_start: 0.8392 (t70) cc_final: 0.8066 (t0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2663 time to fit residues: 143.6457 Evaluate side-chains 302 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS B 660 HIS C 217 GLN C 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.128837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101751 restraints weight = 43842.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104536 restraints weight = 30358.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106598 restraints weight = 22832.978| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6725 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= 0.128 Angle : 0.670 10.330 18529 Z= 0.340 Chirality : 0.045 0.176 2007 Planarity : 0.004 0.051 2364 Dihedral : 4.896 21.037 1813 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1653 helix: 0.14 (0.19), residues: 746 sheet: -1.05 (0.46), residues: 133 loop : -2.58 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 319 HIS 0.005 0.001 HIS A 263 PHE 0.035 0.002 PHE A 161 TYR 0.015 0.001 TYR B 560 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 564) hydrogen bonds : angle 4.87241 ( 1593) covalent geometry : bond 0.00286 (13795) covalent geometry : angle 0.66973 (18529) *********************** 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 381 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.520 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: A 28 TYR cc_start: 0.8355 (t80) cc_final: 0.8069 (t80) REVERT: A 161 PHE cc_start: 0.9235 (m-80) cc_final: 0.8783 (m-80) REVERT: A 165 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8974 (mm-30) REVERT: A 208 TYR cc_start: 0.8716 (t80) cc_final: 0.8311 (t80) REVERT: A 269 ASP cc_start: 0.7612 (m-30) cc_final: 0.7165 (t0) REVERT: A 297 MET cc_start: 0.9099 (mpp) cc_final: 0.8856 (mpp) REVERT: A 357 TRP cc_start: 0.7713 (t60) cc_final: 0.7393 (t60) REVERT: A 382 PHE cc_start: 0.8495 (t80) cc_final: 0.8118 (t80) REVERT: A 406 MET cc_start: 0.8923 (tpt) cc_final: 0.8464 (tpt) REVERT: A 426 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 438 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8559 (ttp80) REVERT: A 467 TYR cc_start: 0.8191 (p90) cc_final: 0.7896 (p90) REVERT: A 503 PHE cc_start: 0.5063 (m-10) cc_final: 0.4690 (m-10) REVERT: A 606 HIS cc_start: 0.6564 (p-80) cc_final: 0.5347 (p-80) REVERT: A 624 CYS cc_start: 0.9043 (p) cc_final: 0.8837 (p) REVERT: A 645 PHE cc_start: 0.8532 (t80) cc_final: 0.7823 (t80) REVERT: A 649 GLN cc_start: 0.9367 (pt0) cc_final: 0.9006 (pt0) REVERT: A 651 LYS cc_start: 0.9408 (tppt) cc_final: 0.8689 (mttt) REVERT: A 669 ASN cc_start: 0.8393 (t0) cc_final: 0.8056 (t0) REVERT: A 684 ASN cc_start: 0.9461 (t0) cc_final: 0.9217 (t0) REVERT: B 3 ILE cc_start: 0.8220 (tt) cc_final: 0.7985 (tt) REVERT: B 10 LEU cc_start: 0.8999 (tt) cc_final: 0.8793 (mm) REVERT: B 25 THR cc_start: 0.9162 (p) cc_final: 0.8936 (p) REVERT: B 41 GLU cc_start: 0.8846 (tt0) cc_final: 0.8339 (tm-30) REVERT: B 45 ARG cc_start: 0.8554 (ttp-170) cc_final: 0.8298 (ttp-170) REVERT: B 95 GLU cc_start: 0.8331 (tt0) cc_final: 0.7735 (tm-30) REVERT: B 96 MET cc_start: 0.8399 (mmt) cc_final: 0.7494 (mmt) REVERT: B 172 ILE cc_start: 0.9731 (mt) cc_final: 0.9462 (mm) REVERT: B 175 MET cc_start: 0.9445 (ptp) cc_final: 0.9094 (ptm) REVERT: B 185 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8285 (pptt) REVERT: B 210 MET cc_start: 0.6507 (pmm) cc_final: 0.5821 (pmm) REVERT: B 248 MET cc_start: 0.7894 (tpp) cc_final: 0.7565 (tpp) REVERT: B 348 ASN cc_start: 0.9004 (p0) cc_final: 0.8125 (t0) REVERT: B 378 ARG cc_start: 0.8734 (mmt180) cc_final: 0.8452 (mmt180) REVERT: B 397 MET cc_start: 0.7540 (mmp) cc_final: 0.6188 (tpt) REVERT: B 423 MET cc_start: 0.7839 (mtp) cc_final: 0.6606 (mtp) REVERT: B 426 ASN cc_start: 0.9207 (m-40) cc_final: 0.8933 (m110) REVERT: B 462 MET cc_start: 0.8594 (tpp) cc_final: 0.8288 (tpp) REVERT: B 491 PHE cc_start: 0.8232 (p90) cc_final: 0.7671 (p90) REVERT: B 528 MET cc_start: 0.6382 (tmm) cc_final: 0.5981 (tmm) REVERT: B 665 ARG cc_start: 0.7924 (tpt90) cc_final: 0.7100 (tpp80) REVERT: B 691 MET cc_start: 0.8486 (mtp) cc_final: 0.8265 (mtp) REVERT: C 7 LEU cc_start: 0.8874 (mm) cc_final: 0.8473 (mm) REVERT: C 10 GLU cc_start: 0.9297 (pt0) cc_final: 0.8809 (pp20) REVERT: C 126 PHE cc_start: 0.8347 (m-10) cc_final: 0.8143 (m-80) REVERT: C 134 GLU cc_start: 0.8529 (tp30) cc_final: 0.8032 (pp20) REVERT: C 140 MET cc_start: 0.8641 (tmm) cc_final: 0.7698 (tmm) REVERT: C 171 MET cc_start: 0.6511 (mmm) cc_final: 0.6171 (mmt) REVERT: C 726 ASP cc_start: 0.8421 (t70) cc_final: 0.8048 (t0) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.2600 time to fit residues: 142.6521 Evaluate side-chains 317 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 101 optimal weight: 0.0980 chunk 64 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS A 606 HIS ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4029 r_free = 0.4029 target = 0.127001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100225 restraints weight = 44138.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102925 restraints weight = 30530.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.104843 restraints weight = 23014.987| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.7048 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= 0.150 Angle : 0.699 10.135 18529 Z= 0.358 Chirality : 0.045 0.237 2007 Planarity : 0.005 0.076 2364 Dihedral : 4.952 21.534 1813 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1653 helix: 0.17 (0.19), residues: 748 sheet: -1.06 (0.47), residues: 131 loop : -2.49 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 386 HIS 0.007 0.001 HIS A 263 PHE 0.048 0.002 PHE C 142 TYR 0.040 0.002 TYR A 419 ARG 0.009 0.001 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 564) hydrogen bonds : angle 4.93124 ( 1593) covalent geometry : bond 0.00336 (13795) covalent geometry : angle 0.69907 (18529) *********************** 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 373 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.740 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 28 TYR cc_start: 0.8499 (t80) cc_final: 0.8264 (t80) REVERT: A 116 TYR cc_start: 0.8035 (t80) cc_final: 0.7368 (m-80) REVERT: A 161 PHE cc_start: 0.9281 (m-80) cc_final: 0.8800 (m-80) REVERT: A 208 TYR cc_start: 0.8704 (t80) cc_final: 0.8376 (t80) REVERT: A 269 ASP cc_start: 0.7879 (m-30) cc_final: 0.7336 (t0) REVERT: A 297 MET cc_start: 0.9113 (mpp) cc_final: 0.8829 (mpp) REVERT: A 357 TRP cc_start: 0.7734 (t60) cc_final: 0.7352 (t60) REVERT: A 382 PHE cc_start: 0.8398 (t80) cc_final: 0.8078 (t80) REVERT: A 406 MET cc_start: 0.8807 (tpt) cc_final: 0.8360 (tpt) REVERT: A 425 GLU cc_start: 0.8806 (pp20) cc_final: 0.8463 (pp20) REVERT: A 426 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 467 TYR cc_start: 0.8061 (p90) cc_final: 0.7830 (p90) REVERT: A 503 PHE cc_start: 0.5159 (m-10) cc_final: 0.4754 (m-10) REVERT: A 579 GLN cc_start: 0.9066 (tt0) cc_final: 0.8816 (tt0) REVERT: A 643 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8150 (mm-30) REVERT: A 645 PHE cc_start: 0.8580 (t80) cc_final: 0.7957 (t80) REVERT: A 649 GLN cc_start: 0.9412 (pt0) cc_final: 0.9101 (pt0) REVERT: A 651 LYS cc_start: 0.9405 (tppt) cc_final: 0.9038 (mttt) REVERT: A 669 ASN cc_start: 0.8463 (t0) cc_final: 0.8189 (t0) REVERT: A 684 ASN cc_start: 0.9455 (t0) cc_final: 0.9171 (t0) REVERT: B 25 THR cc_start: 0.9187 (p) cc_final: 0.8918 (p) REVERT: B 40 MET cc_start: 0.8932 (ptp) cc_final: 0.8577 (ptm) REVERT: B 41 GLU cc_start: 0.8870 (tt0) cc_final: 0.8324 (tm-30) REVERT: B 95 GLU cc_start: 0.8316 (tt0) cc_final: 0.7803 (tm-30) REVERT: B 96 MET cc_start: 0.8277 (mmt) cc_final: 0.7489 (mmt) REVERT: B 130 GLN cc_start: 0.8936 (mt0) cc_final: 0.8360 (mm-40) REVERT: B 226 ILE cc_start: 0.7773 (mp) cc_final: 0.7562 (mp) REVERT: B 248 MET cc_start: 0.8002 (tpp) cc_final: 0.7720 (tpp) REVERT: B 323 MET cc_start: 0.7782 (mmt) cc_final: 0.7144 (mmp) REVERT: B 348 ASN cc_start: 0.9067 (p0) cc_final: 0.8221 (t0) REVERT: B 378 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8479 (mmt180) REVERT: B 423 MET cc_start: 0.7926 (mtp) cc_final: 0.6756 (mtp) REVERT: B 426 ASN cc_start: 0.9287 (m-40) cc_final: 0.8964 (m110) REVERT: B 491 PHE cc_start: 0.8131 (p90) cc_final: 0.7537 (p90) REVERT: B 665 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7052 (tpp80) REVERT: B 691 MET cc_start: 0.8478 (mtp) cc_final: 0.8274 (mtp) REVERT: B 710 MET cc_start: 0.7421 (mmt) cc_final: 0.7066 (mmt) REVERT: C 7 LEU cc_start: 0.8924 (mm) cc_final: 0.8575 (mm) REVERT: C 10 GLU cc_start: 0.9287 (pt0) cc_final: 0.8803 (pp20) REVERT: C 126 PHE cc_start: 0.8297 (m-10) cc_final: 0.8084 (m-80) REVERT: C 134 GLU cc_start: 0.8546 (tp30) cc_final: 0.8060 (pp20) REVERT: C 171 MET cc_start: 0.6469 (mmm) cc_final: 0.6118 (mmt) REVERT: C 726 ASP cc_start: 0.8420 (t70) cc_final: 0.8029 (t70) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2717 time to fit residues: 144.7010 Evaluate side-chains 307 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 142 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 660 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.128848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101678 restraints weight = 43866.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104494 restraints weight = 30355.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.106533 restraints weight = 22809.207| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.7197 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= 0.129 Angle : 0.684 10.156 18529 Z= 0.349 Chirality : 0.045 0.240 2007 Planarity : 0.005 0.103 2364 Dihedral : 4.891 21.105 1813 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1653 helix: 0.23 (0.19), residues: 744 sheet: -0.99 (0.47), residues: 131 loop : -2.47 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 386 HIS 0.005 0.001 HIS A 263 PHE 0.035 0.002 PHE C 142 TYR 0.033 0.002 TYR A 419 ARG 0.007 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 564) hydrogen bonds : angle 4.79926 ( 1593) covalent geometry : bond 0.00292 (13795) covalent geometry : angle 0.68422 (18529) ********************** 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 377 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.676 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: 0.8051 (t80) cc_final: 0.7356 (m-80) REVERT: A 161 PHE cc_start: 0.9253 (m-80) cc_final: 0.8972 (m-80) REVERT: A 208 TYR cc_start: 0.8692 (t80) cc_final: 0.8424 (t80) REVERT: A 269 ASP cc_start: 0.7702 (m-30) cc_final: 0.7387 (t0) REVERT: A 297 MET cc_start: 0.9076 (mpp) cc_final: 0.8822 (mpp) REVERT: A 357 TRP cc_start: 0.7705 (t60) cc_final: 0.7392 (t60) REVERT: A 382 PHE cc_start: 0.8336 (t80) cc_final: 0.7952 (t80) REVERT: A 403 TRP cc_start: 0.8692 (m-90) cc_final: 0.8470 (m-10) REVERT: A 406 MET cc_start: 0.8697 (tpt) cc_final: 0.8277 (tpt) REVERT: A 425 GLU cc_start: 0.8753 (pp20) cc_final: 0.8481 (pp20) REVERT: A 467 TYR cc_start: 0.8041 (p90) cc_final: 0.7721 (p90) REVERT: A 559 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8898 (mtpt) REVERT: A 560 ASN cc_start: 0.9161 (m110) cc_final: 0.8719 (m110) REVERT: A 579 GLN cc_start: 0.9079 (tt0) cc_final: 0.8814 (tt0) REVERT: A 643 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8154 (mm-30) REVERT: A 645 PHE cc_start: 0.8490 (t80) cc_final: 0.7887 (t80) REVERT: A 646 CYS cc_start: 0.8930 (m) cc_final: 0.8680 (m) REVERT: A 649 GLN cc_start: 0.9422 (pt0) cc_final: 0.9094 (pt0) REVERT: A 651 LYS cc_start: 0.9401 (tppt) cc_final: 0.9005 (mttt) REVERT: A 669 ASN cc_start: 0.8467 (t0) cc_final: 0.8166 (t0) REVERT: A 684 ASN cc_start: 0.9430 (t0) cc_final: 0.9148 (t0) REVERT: A 697 LEU cc_start: 0.9479 (tp) cc_final: 0.9239 (tp) REVERT: B 25 THR cc_start: 0.9114 (p) cc_final: 0.8854 (p) REVERT: B 40 MET cc_start: 0.8911 (ptp) cc_final: 0.8661 (ptm) REVERT: B 41 GLU cc_start: 0.8884 (tt0) cc_final: 0.8329 (tm-30) REVERT: B 45 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8388 (ttp-170) REVERT: B 86 ASP cc_start: 0.9145 (t0) cc_final: 0.8944 (t0) REVERT: B 95 GLU cc_start: 0.8295 (tt0) cc_final: 0.7891 (tm-30) REVERT: B 96 MET cc_start: 0.8354 (mmt) cc_final: 0.7307 (mmt) REVERT: B 219 PHE cc_start: 0.8915 (t80) cc_final: 0.8675 (t80) REVERT: B 226 ILE cc_start: 0.7694 (mp) cc_final: 0.7472 (mp) REVERT: B 248 MET cc_start: 0.7952 (tpp) cc_final: 0.7728 (tpp) REVERT: B 348 ASN cc_start: 0.8967 (p0) cc_final: 0.8190 (t0) REVERT: B 378 ARG cc_start: 0.8696 (mmt180) cc_final: 0.8408 (mmt180) REVERT: B 422 VAL cc_start: 0.9116 (m) cc_final: 0.8912 (m) REVERT: B 423 MET cc_start: 0.7956 (mtp) cc_final: 0.6825 (mtp) REVERT: B 426 ASN cc_start: 0.9260 (m-40) cc_final: 0.8920 (m110) REVERT: B 491 PHE cc_start: 0.8208 (p90) cc_final: 0.7573 (p90) REVERT: B 665 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7023 (tpp80) REVERT: B 691 MET cc_start: 0.8462 (mtp) cc_final: 0.8234 (mtp) REVERT: B 692 TYR cc_start: 0.7572 (t80) cc_final: 0.7240 (t80) REVERT: C 7 LEU cc_start: 0.8907 (mm) cc_final: 0.8500 (mm) REVERT: C 10 GLU cc_start: 0.9277 (pt0) cc_final: 0.8804 (pp20) REVERT: C 134 GLU cc_start: 0.8537 (tp30) cc_final: 0.8009 (pp20) REVERT: C 171 MET cc_start: 0.6462 (mmm) cc_final: 0.6065 (mmt) REVERT: C 212 PHE cc_start: 0.8450 (m-80) cc_final: 0.7811 (m-80) REVERT: C 726 ASP cc_start: 0.8388 (t70) cc_final: 0.7961 (t70) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2655 time to fit residues: 143.9826 Evaluate side-chains 321 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 154 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100516 restraints weight = 44183.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103534 restraints weight = 29427.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105762 restraints weight = 21603.851| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.003 0.054 13795 Z= 0.128 Angle : 0.693 9.976 18529 Z= 0.352 Chirality : 0.046 0.225 2007 Planarity : 0.005 0.065 2364 Dihedral : 4.840 20.590 1813 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1653 helix: 0.21 (0.19), residues: 747 sheet: -1.02 (0.46), residues: 136 loop : -2.43 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 386 HIS 0.006 0.001 HIS A 515 PHE 0.029 0.002 PHE A 161 TYR 0.034 0.002 TYR A 419 ARG 0.007 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 564) hydrogen bonds : angle 4.76547 ( 1593) covalent geometry : bond 0.00286 (13795) covalent geometry : angle 0.69327 (18529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.13 seconds wall clock time: 85 minutes 5.99 seconds (5105.99 seconds total)