Starting phenix.real_space_refine on Sat Aug 23 18:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kuv_9888/08_2025/6kuv_9888_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kuv_9888/08_2025/6kuv_9888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kuv_9888/08_2025/6kuv_9888_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kuv_9888/08_2025/6kuv_9888_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kuv_9888/08_2025/6kuv_9888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kuv_9888/08_2025/6kuv_9888.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 116 5.16 5 C 8629 2.51 5 N 2338 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13720 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5625 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 661} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5599 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 3} Chain: "V" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 285 Classifications: {'RNA': 13} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 8} Time building chain proxies: 3.42, per 1000 atoms: 0.25 Number of scatterers: 13720 At special positions: 0 Unit cell: (110.16, 127.84, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 23 15.00 O 2614 8.00 N 2338 7.00 C 8629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 409.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 48.5% alpha, 7.7% beta 4 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.989A pdb=" N ASN A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 removed outlier: 4.047A pdb=" N ILE A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 150 through 170 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.515A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.186A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.712A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.545A 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: 3.703A 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 565 through 568 removed outlier: 3.584A pdb=" N ARG A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 569 through 589 removed outlier: 4.335A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 637 removed outlier: 3.822A pdb=" N MET A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.601A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.619A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 12 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.782A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.797A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.589A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.543A pdb=" N CYS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.590A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.811A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.752A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.762A 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: 3.642A 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 426 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.726A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.539A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.775A 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 668 through 672 removed outlier: 4.170A pdb=" N LEU B 671 " --> pdb=" O ARG B 668 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 672 " --> pdb=" O THR B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 672' Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.858A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.657A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.642A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.790A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.690A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.722A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.696A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.720A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.220A pdb=" N GLU C 178 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 179' Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.741A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.543A pdb=" N ARG C 235 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU C 237 " --> pdb=" O GLU C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.561A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 243' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.341A pdb=" N GLU A 105 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE A 133 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.339A 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 removed outlier: 3.555A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.358A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.874A 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 601 through 604 Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.538A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.502A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.601A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 567 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3745 1.33 - 1.46: 2605 1.46 - 1.58: 7448 1.58 - 1.70: 44 1.70 - 1.82: 192 Bond restraints: 14034 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.378 -0.045 8.40e-03 1.42e+04 2.84e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.27e-02 6.20e+03 1.76e+01 bond pdb=" C LEU B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.12e+00 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.25e-02 6.40e+03 5.00e+00 ... (remaining 14029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18430 2.04 - 4.09: 448 4.09 - 6.13: 60 6.13 - 8.18: 25 8.18 - 10.22: 3 Bond angle restraints: 18966 Sorted by residual: angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.53 106.94 6.59 9.80e-01 1.04e+00 4.52e+01 angle pdb=" N ILE B 393 " pdb=" CA ILE B 393 " pdb=" C ILE B 393 " ideal model delta sigma weight residual 113.20 107.64 5.56 9.60e-01 1.09e+00 3.35e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.42 -4.85 1.25e+00 6.40e-01 1.51e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 121.80 -7.70 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLN A 358 " pdb=" CB GLN A 358 " pdb=" CG GLN A 358 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 ... (remaining 18961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8531 35.86 - 71.72: 82 71.72 - 107.57: 8 107.57 - 143.43: 0 143.43 - 179.29: 4 Dihedral angle restraints: 8625 sinusoidal: 3837 harmonic: 4788 Sorted by residual: dihedral pdb=" O4' U V 5 " pdb=" C1' U V 5 " pdb=" N1 U V 5 " pdb=" C2 U V 5 " ideal model delta sinusoidal sigma weight residual 232.00 52.71 179.29 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 7 " pdb=" C1' C R 7 " pdb=" N1 C R 7 " pdb=" C2 C R 7 " ideal model delta sinusoidal sigma weight residual -128.00 51.08 -179.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 4 " pdb=" C1' U R 4 " pdb=" N1 U R 4 " pdb=" C2 U R 4 " ideal model delta sinusoidal sigma weight residual -128.00 48.06 -176.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1660 0.058 - 0.116: 353 0.116 - 0.174: 57 0.174 - 0.232: 5 0.232 - 0.290: 4 Chirality restraints: 2079 Sorted by residual: 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 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2076 not shown) Planarity restraints: 2333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 422 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.21e+01 pdb=" C LYS A 422 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS A 422 " 0.023 2.00e-02 2.50e+03 pdb=" N MET A 423 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 423 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C MET A 423 " 0.060 2.00e-02 2.50e+03 pdb=" O MET A 423 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS A 424 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 628 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE A 628 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 628 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 629 " -0.020 2.00e-02 2.50e+03 ... (remaining 2330 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1198 2.75 - 3.28: 12752 3.28 - 3.82: 20932 3.82 - 4.36: 25381 4.36 - 4.90: 43484 Nonbonded interactions: 103747 Sorted by model distance: nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.206 3.120 nonbonded pdb=" OE2 GLU A 408 " pdb=" NH2 ARG B 557 " model vdw 2.230 3.120 nonbonded pdb=" OH TYR B 320 " pdb=" OG SER B 417 " model vdw 2.287 3.040 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.289 3.040 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.293 3.040 ... (remaining 103742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14034 Z= 0.191 Angle : 0.793 10.221 18966 Z= 0.447 Chirality : 0.050 0.290 2079 Planarity : 0.006 0.065 2333 Dihedral : 11.910 179.287 5517 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 0.28 % Allowed : 2.28 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.84 (0.15), residues: 1618 helix: -3.33 (0.12), residues: 716 sheet: -1.95 (0.45), residues: 138 loop : -3.31 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 438 TYR 0.017 0.002 TYR B 38 PHE 0.022 0.002 PHE B 420 TRP 0.032 0.003 TRP A 386 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00348 (14034) covalent geometry : angle 0.79326 (18966) hydrogen bonds : bond 0.14342 ( 578) hydrogen bonds : angle 9.53900 ( 1627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 598 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4421 (ttp80) cc_final: 0.3887 (mtm-85) REVERT: A 43 GLN cc_start: 0.7455 (tt0) cc_final: 0.7218 (tp-100) REVERT: A 121 PHE cc_start: 0.4748 (t80) cc_final: 0.4488 (t80) REVERT: A 291 PHE cc_start: 0.7882 (m-80) cc_final: 0.6786 (m-80) REVERT: A 419 TYR cc_start: 0.7818 (t80) cc_final: 0.7532 (t80) REVERT: A 435 ASN cc_start: 0.7487 (m-40) cc_final: 0.6975 (t0) REVERT: A 457 PHE cc_start: 0.8099 (m-80) cc_final: 0.7546 (m-80) REVERT: A 492 ASN cc_start: 0.6371 (m-40) cc_final: 0.5653 (p0) REVERT: A 578 GLU cc_start: 0.7817 (tt0) cc_final: 0.7124 (tt0) REVERT: A 653 LEU cc_start: 0.8041 (mp) cc_final: 0.7715 (mp) REVERT: B 46 THR cc_start: 0.8474 (m) cc_final: 0.7942 (t) REVERT: B 90 MET cc_start: 0.8749 (ppp) cc_final: 0.8516 (ptm) REVERT: B 138 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6744 (ttm-80) REVERT: B 180 GLU cc_start: 0.6231 (tt0) cc_final: 0.5988 (mp0) REVERT: B 219 PHE cc_start: 0.8465 (t80) cc_final: 0.8028 (t80) REVERT: B 357 PHE cc_start: 0.6732 (p90) cc_final: 0.6365 (p90) REVERT: B 446 ASP cc_start: 0.8334 (p0) cc_final: 0.7588 (p0) REVERT: B 494 THR cc_start: 0.8449 (p) cc_final: 0.8130 (p) REVERT: B 547 MET cc_start: 0.7978 (tpp) cc_final: 0.7712 (tpp) REVERT: B 574 MET cc_start: 0.7858 (mmm) cc_final: 0.7160 (mmm) REVERT: B 610 GLU cc_start: 0.7169 (mp0) cc_final: 0.6591 (mp0) REVERT: C 11 TYR cc_start: 0.7078 (t80) cc_final: 0.6652 (t80) REVERT: C 55 MET cc_start: 0.8904 (mmm) cc_final: 0.8363 (tpp) REVERT: C 156 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8106 (Cg_endo) REVERT: C 178 GLU cc_start: 0.5514 (pp20) cc_final: 0.5108 (pp20) REVERT: C 209 VAL cc_start: 0.9236 (t) cc_final: 0.9035 (t) REVERT: C 225 LEU cc_start: 0.8192 (mt) cc_final: 0.7971 (mt) outliers start: 4 outliers final: 0 residues processed: 602 average time/residue: 0.1405 time to fit residues: 116.5303 Evaluate side-chains 322 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0070 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS A 210 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN B 11 ASN B 70 ASN B 84 ASN B 147 GLN B 383 ASN B 477 ASN B 519 ASN B 572 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135659 restraints weight = 22916.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138402 restraints weight = 14975.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140226 restraints weight = 11073.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141628 restraints weight = 8959.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142409 restraints weight = 7632.762| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14034 Z= 0.124 Angle : 0.606 8.700 18966 Z= 0.313 Chirality : 0.041 0.186 2079 Planarity : 0.005 0.054 2333 Dihedral : 13.156 179.875 2115 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 0.14 % Allowed : 3.38 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.18), residues: 1618 helix: -1.06 (0.17), residues: 738 sheet: -1.18 (0.48), residues: 141 loop : -3.07 (0.19), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 133 TYR 0.016 0.001 TYR C 11 PHE 0.014 0.001 PHE B 219 TRP 0.022 0.002 TRP A 357 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00253 (14034) covalent geometry : angle 0.60631 (18966) hydrogen bonds : bond 0.04769 ( 578) hydrogen bonds : angle 5.38056 ( 1627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 409 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4390 (ttp80) cc_final: 0.3514 (mpp-170) REVERT: A 120 LYS cc_start: 0.6699 (mmtm) cc_final: 0.6411 (mttp) REVERT: A 291 PHE cc_start: 0.7933 (m-80) cc_final: 0.6795 (m-80) REVERT: A 419 TYR cc_start: 0.7721 (t80) cc_final: 0.7129 (t80) REVERT: A 492 ASN cc_start: 0.6264 (m-40) cc_final: 0.5468 (p0) REVERT: A 578 GLU cc_start: 0.7702 (tt0) cc_final: 0.6861 (tt0) REVERT: A 591 ASN cc_start: 0.7042 (t0) cc_final: 0.6825 (t0) REVERT: A 638 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 653 LEU cc_start: 0.8255 (mp) cc_final: 0.7813 (mp) REVERT: A 697 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8985 (tp) REVERT: B 17 MET cc_start: 0.5893 (mpp) cc_final: 0.5393 (mpp) REVERT: B 77 ASN cc_start: 0.7739 (p0) cc_final: 0.6960 (p0) REVERT: B 85 VAL cc_start: 0.8302 (t) cc_final: 0.8093 (t) REVERT: B 138 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6981 (ttm-80) REVERT: B 178 TRP cc_start: 0.6528 (m-10) cc_final: 0.6322 (m-10) REVERT: B 321 LEU cc_start: 0.8145 (tt) cc_final: 0.7912 (tt) REVERT: B 375 MET cc_start: 0.7482 (mtm) cc_final: 0.7225 (mtp) REVERT: B 381 LEU cc_start: 0.7714 (mp) cc_final: 0.7508 (mt) REVERT: B 388 ASP cc_start: 0.8527 (m-30) cc_final: 0.8258 (m-30) REVERT: B 391 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6987 (pt0) REVERT: B 450 LEU cc_start: 0.9142 (tp) cc_final: 0.8887 (tp) REVERT: B 610 GLU cc_start: 0.7058 (mp0) cc_final: 0.6736 (mp0) REVERT: B 675 MET cc_start: 0.5323 (ppp) cc_final: 0.4770 (ppp) REVERT: C 5 LEU cc_start: 0.6899 (pt) cc_final: 0.6592 (pt) REVERT: C 9 LYS cc_start: 0.7759 (mttt) cc_final: 0.7424 (ptpt) REVERT: C 156 PRO cc_start: 0.8118 (Cg_exo) cc_final: 0.7809 (Cg_endo) REVERT: C 225 LEU cc_start: 0.8556 (mt) cc_final: 0.8216 (mt) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.1210 time to fit residues: 71.8836 Evaluate side-chains 298 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 18 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 222 GLN A 263 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 647 ASN ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130844 restraints weight = 23487.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133458 restraints weight = 15438.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135194 restraints weight = 11383.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136377 restraints weight = 9221.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137087 restraints weight = 7940.664| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14034 Z= 0.175 Angle : 0.660 8.444 18966 Z= 0.341 Chirality : 0.043 0.197 2079 Planarity : 0.004 0.046 2333 Dihedral : 13.043 176.445 2115 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 0.07 % Allowed : 2.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.20), residues: 1618 helix: -0.10 (0.18), residues: 749 sheet: -1.07 (0.48), residues: 144 loop : -2.97 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 748 TYR 0.021 0.002 TYR C 11 PHE 0.017 0.002 PHE A 292 TRP 0.028 0.002 TRP A 386 HIS 0.007 0.002 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00392 (14034) covalent geometry : angle 0.66010 (18966) hydrogen bonds : bond 0.05231 ( 578) hydrogen bonds : angle 4.94346 ( 1627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4773 (ttp80) cc_final: 0.3732 (mpp-170) REVERT: A 26 ARG cc_start: 0.5277 (mtt180) cc_final: 0.5040 (mtt180) REVERT: A 291 PHE cc_start: 0.8387 (m-80) cc_final: 0.7495 (m-10) REVERT: A 297 MET cc_start: 0.5467 (mmp) cc_final: 0.4280 (mpp) REVERT: A 492 ASN cc_start: 0.6519 (m-40) cc_final: 0.5970 (p0) REVERT: A 578 GLU cc_start: 0.7877 (tt0) cc_final: 0.7230 (mt-10) REVERT: A 649 GLN cc_start: 0.8637 (pt0) cc_final: 0.8385 (pt0) REVERT: A 653 LEU cc_start: 0.8544 (mp) cc_final: 0.8199 (mp) REVERT: A 680 CYS cc_start: 0.7931 (t) cc_final: 0.7389 (t) REVERT: B 77 ASN cc_start: 0.8389 (p0) cc_final: 0.7894 (p0) REVERT: B 85 VAL cc_start: 0.8490 (t) cc_final: 0.8191 (t) REVERT: B 138 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.6858 (ttm-80) REVERT: B 157 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7659 (pp30) REVERT: B 166 VAL cc_start: 0.7931 (m) cc_final: 0.7369 (m) REVERT: B 178 TRP cc_start: 0.7006 (m-10) cc_final: 0.6665 (m-10) REVERT: B 258 GLU cc_start: 0.6477 (tp30) cc_final: 0.6070 (mm-30) REVERT: B 310 LYS cc_start: 0.8017 (mmtp) cc_final: 0.7600 (mmmt) REVERT: B 357 PHE cc_start: 0.6694 (p90) cc_final: 0.6037 (p90) REVERT: B 364 LYS cc_start: 0.8330 (mttt) cc_final: 0.7748 (ttpt) REVERT: B 375 MET cc_start: 0.7720 (mtm) cc_final: 0.7297 (mtp) REVERT: B 381 LEU cc_start: 0.8038 (mp) cc_final: 0.7576 (mt) REVERT: B 415 MET cc_start: 0.5287 (mpp) cc_final: 0.4456 (mtm) REVERT: B 423 MET cc_start: 0.7892 (mtp) cc_final: 0.7560 (mtm) REVERT: B 496 MET cc_start: 0.7999 (mtp) cc_final: 0.7762 (mtp) REVERT: B 604 SER cc_start: 0.8842 (m) cc_final: 0.7814 (t) REVERT: B 678 MET cc_start: 0.5434 (mpp) cc_final: 0.5201 (tmm) REVERT: C 5 LEU cc_start: 0.7027 (pt) cc_final: 0.6620 (pt) REVERT: C 9 LYS cc_start: 0.8284 (mttt) cc_final: 0.7687 (ptpt) REVERT: C 163 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 225 LEU cc_start: 0.8392 (mt) cc_final: 0.8149 (mt) outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.1241 time to fit residues: 67.7779 Evaluate side-chains 280 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 242 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN B 70 ASN B 84 ASN B 348 ASN B 477 ASN C 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128180 restraints weight = 23538.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130755 restraints weight = 15628.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132457 restraints weight = 11634.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133470 restraints weight = 9463.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134420 restraints weight = 8249.030| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14034 Z= 0.150 Angle : 0.616 7.778 18966 Z= 0.316 Chirality : 0.042 0.213 2079 Planarity : 0.004 0.041 2333 Dihedral : 13.027 179.056 2115 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.20), residues: 1618 helix: 0.31 (0.19), residues: 758 sheet: -0.98 (0.50), residues: 134 loop : -2.82 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.018 0.001 TYR C 11 PHE 0.020 0.001 PHE B 219 TRP 0.020 0.002 TRP A 386 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00331 (14034) covalent geometry : angle 0.61647 (18966) hydrogen bonds : bond 0.04649 ( 578) hydrogen bonds : angle 4.59339 ( 1627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4825 (ttp80) cc_final: 0.3805 (mpp-170) REVERT: A 43 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7559 (mm-40) REVERT: A 128 MET cc_start: 0.6847 (mpp) cc_final: 0.5983 (mpp) REVERT: A 291 PHE cc_start: 0.8442 (m-80) cc_final: 0.7629 (m-10) REVERT: A 419 TYR cc_start: 0.7639 (t80) cc_final: 0.7275 (t80) REVERT: A 423 MET cc_start: 0.8062 (mtt) cc_final: 0.7330 (mtt) REVERT: A 457 PHE cc_start: 0.7922 (m-80) cc_final: 0.7644 (m-80) REVERT: A 492 ASN cc_start: 0.7120 (m-40) cc_final: 0.5914 (p0) REVERT: A 578 GLU cc_start: 0.7959 (tt0) cc_final: 0.7382 (mt-10) REVERT: A 583 LYS cc_start: 0.8657 (tptp) cc_final: 0.8394 (tptp) REVERT: A 680 CYS cc_start: 0.8090 (t) cc_final: 0.7391 (t) REVERT: B 77 ASN cc_start: 0.8334 (p0) cc_final: 0.7864 (p0) REVERT: B 85 VAL cc_start: 0.8454 (t) cc_final: 0.8190 (t) REVERT: B 101 MET cc_start: 0.7221 (pmm) cc_final: 0.6963 (pmm) REVERT: B 138 ARG cc_start: 0.7431 (mtp-110) cc_final: 0.6831 (ttm-80) REVERT: B 166 VAL cc_start: 0.8256 (m) cc_final: 0.7371 (m) REVERT: B 310 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7695 (mmmt) REVERT: B 364 LYS cc_start: 0.8352 (mttt) cc_final: 0.7783 (ttpt) REVERT: B 375 MET cc_start: 0.7821 (mtm) cc_final: 0.7317 (mtp) REVERT: B 381 LEU cc_start: 0.7923 (mp) cc_final: 0.7690 (mt) REVERT: B 391 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6560 (pt0) REVERT: B 465 LEU cc_start: 0.8897 (mm) cc_final: 0.8376 (mm) REVERT: B 523 ASP cc_start: 0.7749 (m-30) cc_final: 0.7320 (m-30) REVERT: B 604 SER cc_start: 0.8898 (m) cc_final: 0.7887 (t) REVERT: B 682 GLU cc_start: 0.8349 (tt0) cc_final: 0.7543 (tm-30) REVERT: B 686 GLN cc_start: 0.7069 (mm110) cc_final: 0.6607 (mm-40) REVERT: C 9 LYS cc_start: 0.8324 (mttt) cc_final: 0.7745 (ptpp) REVERT: C 163 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 225 LEU cc_start: 0.8360 (mt) cc_final: 0.8154 (mt) REVERT: C 236 MET cc_start: 0.8232 (mmp) cc_final: 0.7850 (mmp) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.1058 time to fit residues: 55.2348 Evaluate side-chains 274 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN C 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132223 restraints weight = 23446.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134770 restraints weight = 15360.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136518 restraints weight = 11367.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137754 restraints weight = 9131.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138533 restraints weight = 7819.627| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14034 Z= 0.121 Angle : 0.588 8.084 18966 Z= 0.300 Chirality : 0.041 0.208 2079 Planarity : 0.003 0.042 2333 Dihedral : 12.996 179.315 2115 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.98 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.21), residues: 1618 helix: 0.55 (0.19), residues: 762 sheet: -0.90 (0.49), residues: 139 loop : -2.74 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 592 TYR 0.013 0.001 TYR B 560 PHE 0.015 0.001 PHE B 219 TRP 0.029 0.001 TRP B 178 HIS 0.003 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00260 (14034) covalent geometry : angle 0.58825 (18966) hydrogen bonds : bond 0.04193 ( 578) hydrogen bonds : angle 4.41773 ( 1627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4457 (ttp80) cc_final: 0.3488 (mpp-170) REVERT: A 43 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 128 MET cc_start: 0.6562 (mpp) cc_final: 0.5560 (mpp) REVERT: A 212 ARG cc_start: 0.7320 (ttm170) cc_final: 0.6216 (ttm170) REVERT: A 291 PHE cc_start: 0.8463 (m-80) cc_final: 0.7720 (m-10) REVERT: A 419 TYR cc_start: 0.7630 (t80) cc_final: 0.7291 (t80) REVERT: A 423 MET cc_start: 0.7850 (mtt) cc_final: 0.7250 (mtt) REVERT: A 457 PHE cc_start: 0.7913 (m-80) cc_final: 0.7663 (m-80) REVERT: A 578 GLU cc_start: 0.7998 (tt0) cc_final: 0.7412 (mt-10) REVERT: A 680 CYS cc_start: 0.8046 (t) cc_final: 0.7407 (t) REVERT: B 4 ASN cc_start: 0.8439 (t0) cc_final: 0.7872 (t0) REVERT: B 77 ASN cc_start: 0.8303 (p0) cc_final: 0.7779 (p0) REVERT: B 85 VAL cc_start: 0.8367 (t) cc_final: 0.8099 (t) REVERT: B 101 MET cc_start: 0.7134 (pmm) cc_final: 0.6772 (pmm) REVERT: B 138 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.6715 (ttm-80) REVERT: B 166 VAL cc_start: 0.8067 (m) cc_final: 0.7570 (m) REVERT: B 310 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7754 (mmmt) REVERT: B 375 MET cc_start: 0.7743 (mtm) cc_final: 0.7153 (mtp) REVERT: B 391 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6534 (pt0) REVERT: B 604 SER cc_start: 0.8996 (m) cc_final: 0.8031 (t) REVERT: B 611 ILE cc_start: 0.8910 (mt) cc_final: 0.8517 (mt) REVERT: C 9 LYS cc_start: 0.8329 (mttt) cc_final: 0.8120 (mttm) REVERT: C 163 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 186 ILE cc_start: 0.5912 (mp) cc_final: 0.5389 (mm) REVERT: C 236 MET cc_start: 0.8289 (mmp) cc_final: 0.8008 (mmp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1090 time to fit residues: 57.2997 Evaluate side-chains 271 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN B 296 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN C 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127191 restraints weight = 23535.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129605 restraints weight = 15596.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131311 restraints weight = 11643.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132443 restraints weight = 9512.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133131 restraints weight = 8258.475| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14034 Z= 0.180 Angle : 0.672 8.502 18966 Z= 0.346 Chirality : 0.043 0.230 2079 Planarity : 0.004 0.053 2333 Dihedral : 13.087 177.367 2115 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.20), residues: 1618 helix: 0.56 (0.19), residues: 759 sheet: -1.34 (0.47), residues: 132 loop : -2.76 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 567 TYR 0.019 0.002 TYR A 315 PHE 0.023 0.002 PHE C 35 TRP 0.020 0.002 TRP A 386 HIS 0.006 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00410 (14034) covalent geometry : angle 0.67229 (18966) hydrogen bonds : bond 0.05014 ( 578) hydrogen bonds : angle 4.61757 ( 1627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4827 (ttp80) cc_final: 0.3700 (mpp-170) REVERT: A 43 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7422 (mm-40) REVERT: A 128 MET cc_start: 0.6692 (mpp) cc_final: 0.6123 (mpp) REVERT: A 212 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6589 (ttm170) REVERT: A 291 PHE cc_start: 0.8618 (m-80) cc_final: 0.7766 (m-10) REVERT: A 353 GLN cc_start: 0.6252 (tm-30) cc_final: 0.6017 (tm-30) REVERT: A 419 TYR cc_start: 0.7697 (t80) cc_final: 0.7387 (t80) REVERT: A 457 PHE cc_start: 0.8040 (m-80) cc_final: 0.7580 (m-80) REVERT: A 574 MET cc_start: 0.6739 (mtm) cc_final: 0.6440 (mtm) REVERT: A 583 LYS cc_start: 0.8703 (tptp) cc_final: 0.8489 (tptp) REVERT: A 680 CYS cc_start: 0.8159 (t) cc_final: 0.7349 (t) REVERT: B 77 ASN cc_start: 0.8377 (p0) cc_final: 0.7878 (p0) REVERT: B 85 VAL cc_start: 0.8450 (t) cc_final: 0.8162 (t) REVERT: B 101 MET cc_start: 0.7371 (pmm) cc_final: 0.6980 (pmm) REVERT: B 138 ARG cc_start: 0.7433 (mtp-110) cc_final: 0.6570 (ttm-80) REVERT: B 157 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 166 VAL cc_start: 0.8039 (m) cc_final: 0.7459 (m) REVERT: B 178 TRP cc_start: 0.6777 (m-10) cc_final: 0.6447 (m-10) REVERT: B 270 GLU cc_start: 0.7965 (mp0) cc_final: 0.7438 (mp0) REVERT: B 310 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7805 (mmmt) REVERT: B 375 MET cc_start: 0.7908 (mtm) cc_final: 0.7183 (mtp) REVERT: B 391 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6602 (pt0) REVERT: B 443 GLN cc_start: 0.8864 (tp40) cc_final: 0.8422 (tp40) REVERT: B 465 LEU cc_start: 0.8927 (mm) cc_final: 0.8350 (mm) REVERT: B 555 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7067 (mm-30) REVERT: B 594 ASP cc_start: 0.8508 (m-30) cc_final: 0.8203 (m-30) REVERT: B 604 SER cc_start: 0.8893 (m) cc_final: 0.7899 (t) REVERT: B 681 GLU cc_start: 0.6590 (tm-30) cc_final: 0.5855 (tm-30) REVERT: C 9 LYS cc_start: 0.8326 (mttt) cc_final: 0.8003 (mttm) REVERT: C 186 ILE cc_start: 0.5704 (mp) cc_final: 0.4338 (mm) REVERT: C 225 LEU cc_start: 0.8342 (mt) cc_final: 0.8020 (mt) REVERT: C 236 MET cc_start: 0.8836 (mmp) cc_final: 0.8579 (mmp) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.1061 time to fit residues: 52.7042 Evaluate side-chains 269 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 73 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 348 ASN B 426 ASN C 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129417 restraints weight = 23283.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131957 restraints weight = 15261.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133647 restraints weight = 11288.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134815 restraints weight = 9145.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135497 restraints weight = 7884.496| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14034 Z= 0.124 Angle : 0.630 10.290 18966 Z= 0.316 Chirality : 0.042 0.227 2079 Planarity : 0.004 0.051 2333 Dihedral : 13.042 179.210 2115 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.21), residues: 1618 helix: 0.78 (0.19), residues: 748 sheet: -1.34 (0.45), residues: 143 loop : -2.60 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 26 TYR 0.017 0.001 TYR B 560 PHE 0.020 0.001 PHE A 42 TRP 0.032 0.002 TRP C 172 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00274 (14034) covalent geometry : angle 0.62960 (18966) hydrogen bonds : bond 0.04200 ( 578) hydrogen bonds : angle 4.42837 ( 1627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4582 (ttp80) cc_final: 0.3565 (mpp-170) REVERT: A 43 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7372 (mm-40) REVERT: A 212 ARG cc_start: 0.7298 (ttm170) cc_final: 0.6442 (ttm170) REVERT: A 291 PHE cc_start: 0.8524 (m-80) cc_final: 0.7779 (m-80) REVERT: A 297 MET cc_start: 0.5715 (mmt) cc_final: 0.5178 (mpp) REVERT: A 419 TYR cc_start: 0.7604 (t80) cc_final: 0.7313 (t80) REVERT: A 457 PHE cc_start: 0.8024 (m-80) cc_final: 0.7560 (m-80) REVERT: A 590 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 77 ASN cc_start: 0.8335 (p0) cc_final: 0.7805 (p0) REVERT: B 85 VAL cc_start: 0.8465 (t) cc_final: 0.8159 (t) REVERT: B 101 MET cc_start: 0.7250 (pmm) cc_final: 0.6735 (pmm) REVERT: B 138 ARG cc_start: 0.7273 (mtp-110) cc_final: 0.6511 (ttm-80) REVERT: B 166 VAL cc_start: 0.8062 (m) cc_final: 0.7520 (m) REVERT: B 176 MET cc_start: 0.7461 (mtp) cc_final: 0.7125 (mtm) REVERT: B 178 TRP cc_start: 0.6782 (m-10) cc_final: 0.6580 (m-10) REVERT: B 259 THR cc_start: 0.8316 (p) cc_final: 0.7578 (t) REVERT: B 310 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7761 (mmmt) REVERT: B 391 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6809 (pt0) REVERT: B 477 ASN cc_start: 0.7920 (m-40) cc_final: 0.7620 (m110) REVERT: B 555 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 604 SER cc_start: 0.8971 (m) cc_final: 0.7981 (t) REVERT: C 9 LYS cc_start: 0.8221 (mttt) cc_final: 0.7889 (mtpp) REVERT: C 225 LEU cc_start: 0.8274 (mt) cc_final: 0.8003 (mt) REVERT: C 236 MET cc_start: 0.8848 (mmp) cc_final: 0.8294 (mmt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.0976 time to fit residues: 49.9265 Evaluate side-chains 260 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS A 638 ASN B 157 GLN B 296 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 348 ASN C 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128235 restraints weight = 23307.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130663 restraints weight = 15441.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132204 restraints weight = 11563.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133481 restraints weight = 9436.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134161 restraints weight = 8136.749| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14034 Z= 0.162 Angle : 0.670 9.554 18966 Z= 0.340 Chirality : 0.043 0.225 2079 Planarity : 0.004 0.061 2333 Dihedral : 13.093 178.320 2115 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer: Outliers : 0.14 % Allowed : 0.90 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.20), residues: 1618 helix: 0.74 (0.19), residues: 756 sheet: -1.53 (0.46), residues: 133 loop : -2.60 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.027 0.002 TYR A 419 PHE 0.017 0.002 PHE C 35 TRP 0.023 0.002 TRP C 172 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00369 (14034) covalent geometry : angle 0.67042 (18966) hydrogen bonds : bond 0.04703 ( 578) hydrogen bonds : angle 4.51112 ( 1627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 328 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4674 (ttp80) cc_final: 0.3578 (mpp-170) REVERT: A 26 ARG cc_start: 0.6416 (tpp-160) cc_final: 0.6001 (mtt180) REVERT: A 43 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 128 MET cc_start: 0.6579 (mpp) cc_final: 0.5966 (mpp) REVERT: A 212 ARG cc_start: 0.7271 (ttm170) cc_final: 0.6634 (ttm170) REVERT: A 291 PHE cc_start: 0.8592 (m-80) cc_final: 0.7923 (m-80) REVERT: A 297 MET cc_start: 0.5787 (mmt) cc_final: 0.5475 (mpp) REVERT: A 457 PHE cc_start: 0.8107 (m-80) cc_final: 0.7632 (m-80) REVERT: A 590 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 77 ASN cc_start: 0.8333 (p0) cc_final: 0.7828 (p0) REVERT: B 85 VAL cc_start: 0.8530 (t) cc_final: 0.8221 (t) REVERT: B 101 MET cc_start: 0.7265 (pmm) cc_final: 0.6739 (pmm) REVERT: B 138 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6588 (ttm-80) REVERT: B 157 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7326 (pp30) REVERT: B 166 VAL cc_start: 0.8046 (m) cc_final: 0.7448 (m) REVERT: B 176 MET cc_start: 0.7690 (mtp) cc_final: 0.7332 (mtm) REVERT: B 270 GLU cc_start: 0.7883 (mp0) cc_final: 0.7603 (mp0) REVERT: B 310 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7916 (mmmt) REVERT: B 376 LYS cc_start: 0.8287 (tptm) cc_final: 0.8015 (tptm) REVERT: B 391 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6752 (pt0) REVERT: B 477 ASN cc_start: 0.8026 (m-40) cc_final: 0.7691 (m110) REVERT: B 555 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 594 ASP cc_start: 0.8565 (m-30) cc_final: 0.8153 (m-30) REVERT: B 604 SER cc_start: 0.9068 (m) cc_final: 0.8005 (t) REVERT: C 9 LYS cc_start: 0.8273 (mttt) cc_final: 0.8011 (mtpp) REVERT: C 225 LEU cc_start: 0.8263 (mt) cc_final: 0.7954 (mt) REVERT: C 236 MET cc_start: 0.8992 (mmp) cc_final: 0.8780 (mmp) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.0928 time to fit residues: 46.4348 Evaluate side-chains 266 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 153 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 348 ASN C 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131547 restraints weight = 23335.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134090 restraints weight = 15284.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135829 restraints weight = 11328.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136836 restraints weight = 9161.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137804 restraints weight = 7951.745| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14034 Z= 0.125 Angle : 0.645 9.566 18966 Z= 0.322 Chirality : 0.042 0.231 2079 Planarity : 0.004 0.056 2333 Dihedral : 13.050 179.317 2115 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.58 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.21), residues: 1618 helix: 0.80 (0.19), residues: 754 sheet: -1.44 (0.46), residues: 133 loop : -2.51 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.019 0.001 TYR A 419 PHE 0.021 0.001 PHE C 35 TRP 0.059 0.002 TRP B 178 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00275 (14034) covalent geometry : angle 0.64512 (18966) hydrogen bonds : bond 0.04259 ( 578) hydrogen bonds : angle 4.36441 ( 1627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4481 (ttp80) cc_final: 0.3391 (mpp-170) REVERT: A 26 ARG cc_start: 0.6331 (tpp-160) cc_final: 0.5866 (mtt180) REVERT: A 43 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7159 (mm110) REVERT: A 128 MET cc_start: 0.6656 (mpp) cc_final: 0.6397 (mpp) REVERT: A 212 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6766 (ttm170) REVERT: A 291 PHE cc_start: 0.8468 (m-80) cc_final: 0.7854 (m-10) REVERT: A 314 MET cc_start: 0.7078 (ppp) cc_final: 0.6404 (ppp) REVERT: A 323 LYS cc_start: 0.8295 (ptpt) cc_final: 0.7945 (tttt) REVERT: A 419 TYR cc_start: 0.7726 (t80) cc_final: 0.7502 (t80) REVERT: A 457 PHE cc_start: 0.7981 (m-80) cc_final: 0.7522 (m-80) REVERT: A 590 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 671 LYS cc_start: 0.7538 (tppt) cc_final: 0.7335 (pttt) REVERT: B 4 ASN cc_start: 0.8063 (t0) cc_final: 0.7368 (t0) REVERT: B 77 ASN cc_start: 0.8247 (p0) cc_final: 0.7763 (p0) REVERT: B 101 MET cc_start: 0.7543 (pmm) cc_final: 0.6954 (pmm) REVERT: B 138 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.6542 (ttm-80) REVERT: B 157 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7978 (pp30) REVERT: B 176 MET cc_start: 0.7684 (mtp) cc_final: 0.7278 (mtm) REVERT: B 178 TRP cc_start: 0.6715 (m-10) cc_final: 0.6402 (m-10) REVERT: B 310 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7848 (mmmt) REVERT: B 376 LYS cc_start: 0.8308 (tptm) cc_final: 0.7884 (tptm) REVERT: B 391 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6721 (pt0) REVERT: B 400 GLU cc_start: 0.6504 (mp0) cc_final: 0.6198 (mp0) REVERT: B 436 ASN cc_start: 0.7593 (m-40) cc_final: 0.7380 (m-40) REVERT: B 467 PHE cc_start: 0.9331 (t80) cc_final: 0.9008 (t80) REVERT: B 477 ASN cc_start: 0.8044 (m-40) cc_final: 0.7659 (m110) REVERT: B 555 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 604 SER cc_start: 0.8999 (m) cc_final: 0.7982 (t) REVERT: C 84 SER cc_start: 0.7419 (m) cc_final: 0.7091 (t) REVERT: C 225 LEU cc_start: 0.8223 (mt) cc_final: 0.7920 (mt) REVERT: C 236 MET cc_start: 0.8887 (mmp) cc_final: 0.8407 (mmp) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.1053 time to fit residues: 53.9618 Evaluate side-chains 279 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 41 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS A 638 ASN B 84 ASN B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.155095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127234 restraints weight = 23460.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129690 restraints weight = 15697.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131388 restraints weight = 11828.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132555 restraints weight = 9662.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132962 restraints weight = 8373.189| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14034 Z= 0.132 Angle : 0.658 10.367 18966 Z= 0.329 Chirality : 0.043 0.222 2079 Planarity : 0.004 0.055 2333 Dihedral : 13.059 179.495 2115 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.21), residues: 1618 helix: 0.92 (0.19), residues: 743 sheet: -1.31 (0.45), residues: 140 loop : -2.51 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 216 TYR 0.025 0.001 TYR A 419 PHE 0.013 0.001 PHE A 42 TRP 0.047 0.002 TRP B 178 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00297 (14034) covalent geometry : angle 0.65834 (18966) hydrogen bonds : bond 0.04275 ( 578) hydrogen bonds : angle 4.40746 ( 1627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4469 (ttp80) cc_final: 0.3409 (mpp-170) REVERT: A 26 ARG cc_start: 0.6531 (tpp-160) cc_final: 0.5924 (mtt180) REVERT: A 43 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7389 (mm110) REVERT: A 128 MET cc_start: 0.6640 (mpp) cc_final: 0.6370 (mpp) REVERT: A 212 ARG cc_start: 0.7230 (ttm170) cc_final: 0.7004 (ttm170) REVERT: A 291 PHE cc_start: 0.8472 (m-80) cc_final: 0.7826 (m-10) REVERT: A 323 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7959 (tttt) REVERT: A 408 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6091 (mm-30) REVERT: A 457 PHE cc_start: 0.8067 (m-80) cc_final: 0.7652 (m-80) REVERT: A 590 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 598 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6433 (mm-30) REVERT: A 629 VAL cc_start: 0.8600 (t) cc_final: 0.8375 (t) REVERT: A 671 LYS cc_start: 0.7495 (tppt) cc_final: 0.7268 (pttt) REVERT: B 77 ASN cc_start: 0.8261 (p0) cc_final: 0.7792 (p0) REVERT: B 96 MET cc_start: 0.7788 (mtt) cc_final: 0.7122 (mtm) REVERT: B 101 MET cc_start: 0.7589 (pmm) cc_final: 0.6994 (pmm) REVERT: B 138 ARG cc_start: 0.7241 (mtp-110) cc_final: 0.6530 (ttm-80) REVERT: B 157 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7791 (pp30) REVERT: B 176 MET cc_start: 0.7635 (mtp) cc_final: 0.7248 (mtm) REVERT: B 178 TRP cc_start: 0.6756 (m-10) cc_final: 0.6421 (m-10) REVERT: B 270 GLU cc_start: 0.7818 (mp0) cc_final: 0.7544 (mp0) REVERT: B 310 LYS cc_start: 0.8274 (mmtp) cc_final: 0.8002 (mmmt) REVERT: B 391 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6763 (pt0) REVERT: B 446 ASP cc_start: 0.7648 (p0) cc_final: 0.7016 (t70) REVERT: B 477 ASN cc_start: 0.8016 (m-40) cc_final: 0.7634 (p0) REVERT: B 555 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 604 SER cc_start: 0.9008 (m) cc_final: 0.7877 (t) REVERT: C 84 SER cc_start: 0.7375 (m) cc_final: 0.7124 (t) REVERT: C 225 LEU cc_start: 0.8295 (mt) cc_final: 0.8004 (mt) REVERT: C 236 MET cc_start: 0.8932 (mmp) cc_final: 0.8490 (mmt) outliers start: 2 outliers final: 0 residues processed: 337 average time/residue: 0.1062 time to fit residues: 54.0100 Evaluate side-chains 283 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 128 optimal weight: 0.4980 chunk 100 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A 638 ASN B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132906 restraints weight = 23316.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135377 restraints weight = 15511.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137141 restraints weight = 11549.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138353 restraints weight = 9262.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139023 restraints weight = 7906.712| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14034 Z= 0.123 Angle : 0.663 10.171 18966 Z= 0.330 Chirality : 0.042 0.236 2079 Planarity : 0.004 0.054 2333 Dihedral : 13.022 179.435 2115 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 0.14 % Allowed : 0.21 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.21), residues: 1618 helix: 1.02 (0.19), residues: 743 sheet: -1.23 (0.45), residues: 139 loop : -2.45 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 455 TYR 0.021 0.001 TYR A 419 PHE 0.024 0.001 PHE A 158 TRP 0.041 0.002 TRP B 178 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00271 (14034) covalent geometry : angle 0.66325 (18966) hydrogen bonds : bond 0.04181 ( 578) hydrogen bonds : angle 4.31848 ( 1627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.80 seconds wall clock time: 39 minutes 57.21 seconds (2397.21 seconds total)