Starting phenix.real_space_refine on Thu Jul 31 23:09:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kuv_9888/07_2025/6kuv_9888_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kuv_9888/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kuv_9888/07_2025/6kuv_9888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kuv_9888/07_2025/6kuv_9888.map" model { file = "/net/cci-nas-00/data/ceres_data/6kuv_9888/07_2025/6kuv_9888_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kuv_9888/07_2025/6kuv_9888_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: 8.37, per 1000 atoms: 0.61 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: 3.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 5.31 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: 4.63 Time building geometry restraints manager: 4.29 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.460 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- 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 : 6.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (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 TRP 0.032 0.003 TRP A 386 HIS 0.008 0.001 HIS A 451 PHE 0.022 0.002 PHE B 420 TYR 0.017 0.002 TYR B 38 ARG 0.006 0.001 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.14342 ( 578) hydrogen bonds : angle 9.53900 ( 1627) covalent geometry : bond 0.00348 (14034) covalent geometry : angle 0.79326 (18966) *********************** 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 : 1.414 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: 0.3109 time to fit residues: 255.2024 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 : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 131 HIS A 210 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 515 HIS A 606 HIS A 638 ASN B 84 ASN B 147 GLN B 383 ASN B 477 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132307 restraints weight = 23129.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134946 restraints weight = 15156.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136772 restraints weight = 11274.194| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14034 Z= 0.165 Angle : 0.651 10.251 18966 Z= 0.338 Chirality : 0.043 0.192 2079 Planarity : 0.005 0.054 2333 Dihedral : 13.158 177.713 2115 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.18), residues: 1618 helix: -1.08 (0.17), residues: 742 sheet: -1.07 (0.50), residues: 131 loop : -3.13 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 386 HIS 0.006 0.001 HIS A 451 PHE 0.016 0.002 PHE B 219 TYR 0.018 0.001 TYR B 685 ARG 0.006 0.001 ARG C 133 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 578) hydrogen bonds : angle 5.48997 ( 1627) covalent geometry : bond 0.00360 (14034) covalent geometry : angle 0.65108 (18966) *********************** 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 395 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 392 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4599 (ttp80) cc_final: 0.3563 (mpp-170) REVERT: A 120 LYS cc_start: 0.6879 (mmtm) cc_final: 0.6468 (mttp) REVERT: A 291 PHE cc_start: 0.8217 (m-80) cc_final: 0.6729 (m-10) REVERT: A 419 TYR cc_start: 0.7748 (t80) cc_final: 0.7115 (t80) REVERT: A 435 ASN cc_start: 0.7338 (m-40) cc_final: 0.7135 (t0) REVERT: A 439 GLU cc_start: 0.6868 (tp30) cc_final: 0.6501 (tp30) REVERT: A 492 ASN cc_start: 0.6253 (m-40) cc_final: 0.5412 (p0) REVERT: A 590 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 591 ASN cc_start: 0.7170 (t0) cc_final: 0.6482 (t0) REVERT: A 638 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8161 (t0) REVERT: A 653 LEU cc_start: 0.8445 (mp) cc_final: 0.8031 (mp) REVERT: B 17 MET cc_start: 0.6027 (mpp) cc_final: 0.5556 (mpp) REVERT: B 77 ASN cc_start: 0.7855 (p0) cc_final: 0.7462 (p0) REVERT: B 138 ARG cc_start: 0.7418 (mtp-110) cc_final: 0.6914 (ttm-80) REVERT: B 316 GLN cc_start: 0.8465 (mp10) cc_final: 0.8243 (mp10) REVERT: B 357 PHE cc_start: 0.6518 (p90) cc_final: 0.6273 (p90) REVERT: B 375 MET cc_start: 0.7687 (mtm) cc_final: 0.7460 (mtp) REVERT: B 381 LEU cc_start: 0.7860 (mp) cc_final: 0.7588 (mt) REVERT: B 382 MET cc_start: 0.7363 (mtp) cc_final: 0.6934 (mmt) REVERT: B 388 ASP cc_start: 0.8586 (m-30) cc_final: 0.8002 (m-30) REVERT: B 415 MET cc_start: 0.5422 (mpp) cc_final: 0.5135 (mpp) REVERT: B 610 GLU cc_start: 0.7054 (mp0) cc_final: 0.6768 (mp0) REVERT: B 675 MET cc_start: 0.5483 (ppp) cc_final: 0.4720 (ppp) REVERT: C 5 LEU cc_start: 0.6895 (pt) cc_final: 0.6589 (pt) REVERT: C 9 LYS cc_start: 0.7863 (mttt) cc_final: 0.7470 (ptpt) REVERT: C 156 PRO cc_start: 0.8431 (Cg_exo) cc_final: 0.8130 (Cg_endo) REVERT: C 162 ASN cc_start: 0.6612 (p0) cc_final: 0.5654 (p0) REVERT: C 163 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6815 (tm-30) REVERT: C 225 LEU cc_start: 0.8564 (mt) cc_final: 0.8228 (mt) outliers start: 3 outliers final: 0 residues processed: 393 average time/residue: 0.2601 time to fit residues: 147.4439 Evaluate side-chains 294 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 121 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 263 HIS ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 572 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.159163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131989 restraints weight = 23259.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134598 restraints weight = 15155.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136380 restraints weight = 11182.379| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14034 Z= 0.134 Angle : 0.605 7.624 18966 Z= 0.311 Chirality : 0.042 0.200 2079 Planarity : 0.004 0.048 2333 Dihedral : 13.038 179.158 2115 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1618 helix: -0.07 (0.18), residues: 751 sheet: -0.78 (0.51), residues: 131 loop : -2.95 (0.19), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE A 292 TYR 0.020 0.001 TYR C 11 ARG 0.004 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 578) hydrogen bonds : angle 4.94633 ( 1627) covalent geometry : bond 0.00295 (14034) covalent geometry : angle 0.60519 (18966) *********************** 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 380 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.564 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: 0.4370 (ttp80) cc_final: 0.3430 (mpp-170) REVERT: A 171 MET cc_start: 0.5871 (pmm) cc_final: 0.4887 (pmm) REVERT: A 244 GLU cc_start: 0.7937 (pm20) cc_final: 0.7667 (pm20) REVERT: A 291 PHE cc_start: 0.8373 (m-80) cc_final: 0.7192 (m-10) REVERT: A 419 TYR cc_start: 0.7488 (t80) cc_final: 0.7258 (t80) REVERT: A 423 MET cc_start: 0.7980 (mtt) cc_final: 0.7242 (mtt) REVERT: A 435 ASN cc_start: 0.7429 (m-40) cc_final: 0.7010 (t0) REVERT: A 457 PHE cc_start: 0.8003 (m-80) cc_final: 0.7756 (m-80) REVERT: A 492 ASN cc_start: 0.6662 (m-40) cc_final: 0.5868 (p0) REVERT: A 578 GLU cc_start: 0.7768 (tt0) cc_final: 0.7046 (mt-10) REVERT: A 653 LEU cc_start: 0.8385 (mp) cc_final: 0.8098 (mp) REVERT: B 4 ASN cc_start: 0.8402 (t0) cc_final: 0.7433 (t0) REVERT: B 77 ASN cc_start: 0.7924 (p0) cc_final: 0.7712 (p0) REVERT: B 85 VAL cc_start: 0.8418 (t) cc_final: 0.8213 (t) REVERT: B 138 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6760 (ttm-80) REVERT: B 166 VAL cc_start: 0.7900 (m) cc_final: 0.7355 (m) REVERT: B 178 TRP cc_start: 0.6174 (m-10) cc_final: 0.5554 (m-10) REVERT: B 180 GLU cc_start: 0.6615 (tt0) cc_final: 0.6181 (tm-30) REVERT: B 258 GLU cc_start: 0.6557 (tp30) cc_final: 0.6162 (mm-30) REVERT: B 323 MET cc_start: 0.7075 (tpp) cc_final: 0.6812 (tpp) REVERT: B 357 PHE cc_start: 0.6630 (p90) cc_final: 0.6371 (p90) REVERT: B 375 MET cc_start: 0.7679 (mtm) cc_final: 0.7475 (mtp) REVERT: B 381 LEU cc_start: 0.7841 (mp) cc_final: 0.7335 (mt) REVERT: B 391 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6687 (pt0) REVERT: B 415 MET cc_start: 0.5291 (mpp) cc_final: 0.4433 (mtm) REVERT: B 523 ASP cc_start: 0.7757 (m-30) cc_final: 0.7424 (m-30) REVERT: B 604 SER cc_start: 0.8957 (m) cc_final: 0.7898 (t) REVERT: B 610 GLU cc_start: 0.7009 (mp0) cc_final: 0.6635 (mp0) REVERT: C 9 LYS cc_start: 0.8273 (mttt) cc_final: 0.7650 (ptpt) REVERT: C 162 ASN cc_start: 0.6479 (p0) cc_final: 0.5880 (p0) REVERT: C 164 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8226 (mtpp) REVERT: C 225 LEU cc_start: 0.8486 (mt) cc_final: 0.8170 (mt) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2575 time to fit residues: 141.2369 Evaluate side-chains 283 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 125 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 638 ASN A 647 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 = 0.3860 r_free = 0.3860 target = 0.155748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128972 restraints weight = 23305.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131467 restraints weight = 15359.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133085 restraints weight = 11416.306| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14034 Z= 0.175 Angle : 0.656 7.833 18966 Z= 0.336 Chirality : 0.043 0.215 2079 Planarity : 0.004 0.042 2333 Dihedral : 13.036 177.439 2115 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.58 % Rotamer: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1618 helix: 0.23 (0.19), residues: 752 sheet: -1.10 (0.50), residues: 134 loop : -2.86 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 386 HIS 0.008 0.001 HIS A 515 PHE 0.016 0.002 PHE B 420 TYR 0.016 0.002 TYR A 208 ARG 0.010 0.001 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 578) hydrogen bonds : angle 4.88403 ( 1627) covalent geometry : bond 0.00396 (14034) covalent geometry : angle 0.65584 (18966) *********************** 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 362 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4568 (ttp80) cc_final: 0.3613 (mpp-170) REVERT: A 128 MET cc_start: 0.6844 (mpp) cc_final: 0.5996 (mpp) REVERT: A 212 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6913 (ttm170) REVERT: A 291 PHE cc_start: 0.8407 (m-80) cc_final: 0.7430 (m-10) REVERT: A 297 MET cc_start: 0.5452 (mmp) cc_final: 0.4191 (mpp) REVERT: A 435 ASN cc_start: 0.7508 (m-40) cc_final: 0.6948 (t0) REVERT: A 439 GLU cc_start: 0.6857 (tp30) cc_final: 0.6627 (tp30) REVERT: A 457 PHE cc_start: 0.7938 (m-80) cc_final: 0.7582 (m-80) REVERT: A 590 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 655 PHE cc_start: 0.8208 (m-80) cc_final: 0.8007 (m-80) REVERT: A 680 CYS cc_start: 0.8146 (t) cc_final: 0.7491 (t) REVERT: B 37 LYS cc_start: 0.8240 (tttt) cc_final: 0.7825 (ttmm) REVERT: B 77 ASN cc_start: 0.8247 (p0) cc_final: 0.7773 (p0) REVERT: B 85 VAL cc_start: 0.8419 (t) cc_final: 0.8150 (t) REVERT: B 101 MET cc_start: 0.7362 (pmm) cc_final: 0.6991 (pmm) REVERT: B 138 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.6864 (ttm-80) REVERT: B 166 VAL cc_start: 0.8248 (m) cc_final: 0.7682 (m) REVERT: B 176 MET cc_start: 0.6622 (mtm) cc_final: 0.6084 (mtm) REVERT: B 178 TRP cc_start: 0.6905 (m-10) cc_final: 0.6391 (m-10) REVERT: B 335 MET cc_start: 0.7285 (ttp) cc_final: 0.7074 (ptm) REVERT: B 357 PHE cc_start: 0.6705 (p90) cc_final: 0.6317 (p90) REVERT: B 364 LYS cc_start: 0.8375 (mttt) cc_final: 0.7782 (ttpt) REVERT: B 375 MET cc_start: 0.8016 (mtm) cc_final: 0.7402 (mtp) REVERT: B 381 LEU cc_start: 0.7837 (mp) cc_final: 0.7496 (mt) REVERT: B 391 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6890 (pt0) REVERT: B 523 ASP cc_start: 0.7693 (m-30) cc_final: 0.7435 (m-30) REVERT: B 604 SER cc_start: 0.8868 (m) cc_final: 0.8006 (t) REVERT: B 675 MET cc_start: 0.5713 (ppp) cc_final: 0.5163 (ppp) REVERT: B 678 MET cc_start: 0.4977 (tmm) cc_final: 0.4641 (tmm) REVERT: B 682 GLU cc_start: 0.8361 (tt0) cc_final: 0.7804 (tm-30) REVERT: C 5 LEU cc_start: 0.7002 (pt) cc_final: 0.6397 (pt) REVERT: C 9 LYS cc_start: 0.8274 (mttt) cc_final: 0.7802 (ptpt) REVERT: C 94 MET cc_start: 0.6701 (tpp) cc_final: 0.6500 (tpp) REVERT: C 162 ASN cc_start: 0.6703 (p0) cc_final: 0.6168 (p0) REVERT: C 163 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7878 (tm-30) REVERT: C 225 LEU cc_start: 0.8384 (mt) cc_final: 0.8101 (mt) REVERT: C 238 LEU cc_start: 0.7977 (mt) cc_final: 0.7768 (mt) outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.2665 time to fit residues: 138.3022 Evaluate side-chains 282 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 84 ASN B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 477 ASN C 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129874 restraints weight = 23353.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132412 restraints weight = 15669.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133973 restraints weight = 11726.356| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14034 Z= 0.126 Angle : 0.597 8.231 18966 Z= 0.304 Chirality : 0.041 0.211 2079 Planarity : 0.004 0.051 2333 Dihedral : 13.014 179.618 2115 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1618 helix: 0.42 (0.19), residues: 761 sheet: -1.33 (0.47), residues: 148 loop : -2.70 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 357 HIS 0.003 0.001 HIS A 451 PHE 0.018 0.001 PHE A 42 TYR 0.015 0.001 TYR B 560 ARG 0.005 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 578) hydrogen bonds : angle 4.66618 ( 1627) covalent geometry : bond 0.00275 (14034) covalent geometry : angle 0.59704 (18966) *********************** 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 361 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4539 (ttp80) cc_final: 0.3607 (mpp-170) REVERT: A 43 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7519 (mm-40) REVERT: A 128 MET cc_start: 0.6811 (mpp) cc_final: 0.5944 (mpp) REVERT: A 212 ARG cc_start: 0.7235 (ttm170) cc_final: 0.6047 (ttm170) REVERT: A 291 PHE cc_start: 0.8393 (m-80) cc_final: 0.7456 (m-10) REVERT: A 323 LYS cc_start: 0.8230 (ptpt) cc_final: 0.7973 (tttt) REVERT: A 354 GLU cc_start: 0.5757 (tp30) cc_final: 0.5278 (tm-30) REVERT: A 435 ASN cc_start: 0.7499 (m-40) cc_final: 0.6872 (t0) REVERT: A 439 GLU cc_start: 0.6810 (tp30) cc_final: 0.6609 (tp30) REVERT: A 457 PHE cc_start: 0.7955 (m-80) cc_final: 0.7662 (m-80) REVERT: A 578 GLU cc_start: 0.7966 (tt0) cc_final: 0.7664 (mt-10) REVERT: A 655 PHE cc_start: 0.7971 (m-80) cc_final: 0.7757 (m-80) REVERT: A 671 LYS cc_start: 0.7623 (tppt) cc_final: 0.7408 (pttt) REVERT: A 680 CYS cc_start: 0.8070 (t) cc_final: 0.7467 (t) REVERT: B 42 THR cc_start: 0.7715 (m) cc_final: 0.7304 (p) REVERT: B 77 ASN cc_start: 0.8154 (p0) cc_final: 0.7657 (p0) REVERT: B 85 VAL cc_start: 0.8470 (t) cc_final: 0.8169 (t) REVERT: B 101 MET cc_start: 0.7241 (pmm) cc_final: 0.6831 (pmm) REVERT: B 138 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.6838 (ttm-80) REVERT: B 157 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7694 (pp30) REVERT: B 178 TRP cc_start: 0.6947 (m-10) cc_final: 0.6726 (m-10) REVERT: B 310 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7713 (mmmt) REVERT: B 357 PHE cc_start: 0.6690 (p90) cc_final: 0.6358 (p90) REVERT: B 375 MET cc_start: 0.7796 (mtm) cc_final: 0.7449 (mtp) REVERT: B 381 LEU cc_start: 0.7787 (mp) cc_final: 0.7356 (mt) REVERT: B 391 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6928 (pt0) REVERT: B 604 SER cc_start: 0.8816 (m) cc_final: 0.7924 (t) REVERT: B 611 ILE cc_start: 0.8885 (mt) cc_final: 0.8480 (mt) REVERT: B 675 MET cc_start: 0.6015 (ppp) cc_final: 0.5465 (ppp) REVERT: B 682 GLU cc_start: 0.8482 (tt0) cc_final: 0.8097 (tm-30) REVERT: C 9 LYS cc_start: 0.8369 (mttt) cc_final: 0.7945 (mtpp) REVERT: C 51 MET cc_start: 0.8359 (tpp) cc_final: 0.8066 (tpp) REVERT: C 162 ASN cc_start: 0.6603 (p0) cc_final: 0.6344 (p0) REVERT: C 163 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7558 (tm-30) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.2842 time to fit residues: 150.5425 Evaluate side-chains 289 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 84 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 141 optimal weight: 0.0060 chunk 129 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.0170 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 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 = 0.3893 r_free = 0.3893 target = 0.158680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131715 restraints weight = 23546.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134375 restraints weight = 15647.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136091 restraints weight = 11500.617| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14034 Z= 0.114 Angle : 0.598 8.272 18966 Z= 0.302 Chirality : 0.041 0.205 2079 Planarity : 0.004 0.053 2333 Dihedral : 12.955 178.867 2115 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 0.14 % Allowed : 2.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1618 helix: 0.63 (0.19), residues: 756 sheet: -1.14 (0.48), residues: 143 loop : -2.60 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 357 HIS 0.002 0.001 HIS A 451 PHE 0.020 0.001 PHE A 341 TYR 0.024 0.001 TYR A 419 ARG 0.005 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 578) hydrogen bonds : angle 4.53190 ( 1627) covalent geometry : bond 0.00244 (14034) covalent geometry : angle 0.59772 (18966) *********************** 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 371 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4554 (ttp80) cc_final: 0.3610 (mpp-170) REVERT: A 212 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6473 (ttm170) REVERT: A 291 PHE cc_start: 0.8416 (m-80) cc_final: 0.7510 (m-10) REVERT: A 354 GLU cc_start: 0.5605 (tp30) cc_final: 0.5203 (tm-30) REVERT: A 457 PHE cc_start: 0.7922 (m-80) cc_final: 0.7689 (m-80) REVERT: A 578 GLU cc_start: 0.7973 (tt0) cc_final: 0.7655 (mt-10) REVERT: A 653 LEU cc_start: 0.8329 (mp) cc_final: 0.8048 (mp) REVERT: A 671 LYS cc_start: 0.7550 (tppt) cc_final: 0.7345 (pttt) REVERT: B 4 ASN cc_start: 0.8270 (t0) cc_final: 0.7579 (t0) REVERT: B 77 ASN cc_start: 0.8114 (p0) cc_final: 0.7601 (p0) REVERT: B 85 VAL cc_start: 0.8466 (t) cc_final: 0.8149 (t) REVERT: B 101 MET cc_start: 0.7156 (pmm) cc_final: 0.6680 (pmm) REVERT: B 138 ARG cc_start: 0.7268 (mtp-110) cc_final: 0.6692 (ttm-80) REVERT: B 157 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: B 176 MET cc_start: 0.7376 (mtp) cc_final: 0.7086 (mtp) REVERT: B 310 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7819 (mmmt) REVERT: B 312 ASN cc_start: 0.8317 (m-40) cc_final: 0.7876 (m-40) REVERT: B 357 PHE cc_start: 0.6642 (p90) cc_final: 0.6174 (p90) REVERT: B 375 MET cc_start: 0.7748 (mtm) cc_final: 0.7430 (mtp) REVERT: B 381 LEU cc_start: 0.7643 (mp) cc_final: 0.7416 (mt) REVERT: B 391 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7012 (pt0) REVERT: B 523 ASP cc_start: 0.7749 (m-30) cc_final: 0.6883 (m-30) REVERT: B 604 SER cc_start: 0.8796 (m) cc_final: 0.7858 (t) REVERT: B 675 MET cc_start: 0.6931 (ppp) cc_final: 0.6546 (ppp) REVERT: B 681 GLU cc_start: 0.7982 (pp20) cc_final: 0.7389 (pp20) REVERT: B 682 GLU cc_start: 0.8315 (tt0) cc_final: 0.8081 (tt0) REVERT: C 9 LYS cc_start: 0.8342 (mttt) cc_final: 0.7768 (ptpt) REVERT: C 11 TYR cc_start: 0.7288 (t80) cc_final: 0.7077 (t80) REVERT: C 73 ILE cc_start: 0.7876 (pt) cc_final: 0.7556 (tp) REVERT: C 162 ASN cc_start: 0.6860 (p0) cc_final: 0.6344 (p0) REVERT: C 163 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 225 LEU cc_start: 0.8099 (mt) cc_final: 0.7777 (mt) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.2510 time to fit residues: 135.8838 Evaluate side-chains 282 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 140 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 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 = 0.3891 r_free = 0.3891 target = 0.158461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131650 restraints weight = 23420.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134182 restraints weight = 15420.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135907 restraints weight = 11388.420| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14034 Z= 0.120 Angle : 0.615 8.325 18966 Z= 0.311 Chirality : 0.042 0.207 2079 Planarity : 0.004 0.054 2333 Dihedral : 12.942 179.962 2115 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1618 helix: 0.71 (0.19), residues: 754 sheet: -1.24 (0.45), residues: 147 loop : -2.51 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 178 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.001 PHE A 42 TYR 0.030 0.001 TYR A 419 ARG 0.006 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 578) hydrogen bonds : angle 4.45737 ( 1627) covalent geometry : bond 0.00263 (14034) covalent geometry : angle 0.61460 (18966) *********************** 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 351 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4560 (ttp80) cc_final: 0.3607 (mpp-170) REVERT: A 43 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7434 (mm-40) REVERT: A 128 MET cc_start: 0.6399 (mpp) cc_final: 0.6156 (mpp) REVERT: A 291 PHE cc_start: 0.8442 (m-80) cc_final: 0.7599 (m-10) REVERT: A 354 GLU cc_start: 0.5531 (tp30) cc_final: 0.5313 (tm-30) REVERT: A 424 CYS cc_start: 0.7789 (t) cc_final: 0.7535 (t) REVERT: A 457 PHE cc_start: 0.7945 (m-80) cc_final: 0.7650 (m-80) REVERT: A 671 LYS cc_start: 0.7642 (tppt) cc_final: 0.7322 (pttt) REVERT: B 4 ASN cc_start: 0.8429 (t0) cc_final: 0.7602 (t0) REVERT: B 77 ASN cc_start: 0.8212 (p0) cc_final: 0.7764 (p0) REVERT: B 85 VAL cc_start: 0.8510 (t) cc_final: 0.8197 (t) REVERT: B 101 MET cc_start: 0.7348 (pmm) cc_final: 0.6657 (pmm) REVERT: B 138 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6779 (ttm-80) REVERT: B 157 GLN cc_start: 0.8162 (pp30) cc_final: 0.7678 (pp30) REVERT: B 176 MET cc_start: 0.7449 (mtp) cc_final: 0.7193 (mtm) REVERT: B 310 LYS cc_start: 0.8213 (mmtp) cc_final: 0.7847 (mmmt) REVERT: B 335 MET cc_start: 0.7203 (ttm) cc_final: 0.6472 (ttp) REVERT: B 375 MET cc_start: 0.7962 (mtm) cc_final: 0.7429 (mtp) REVERT: B 391 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7136 (pt0) REVERT: B 445 SER cc_start: 0.8382 (p) cc_final: 0.8167 (p) REVERT: B 604 SER cc_start: 0.8834 (m) cc_final: 0.7856 (t) REVERT: B 678 MET cc_start: 0.5100 (tmm) cc_final: 0.4696 (tmm) REVERT: C 9 LYS cc_start: 0.8262 (mttt) cc_final: 0.7768 (ptpt) REVERT: C 186 ILE cc_start: 0.6662 (mm) cc_final: 0.6196 (mm) REVERT: C 225 LEU cc_start: 0.8028 (mt) cc_final: 0.7707 (mt) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.3132 time to fit residues: 163.3819 Evaluate side-chains 276 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 157 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN C 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127479 restraints weight = 23506.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129936 restraints weight = 15734.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131633 restraints weight = 11756.039| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14034 Z= 0.139 Angle : 0.642 8.472 18966 Z= 0.323 Chirality : 0.042 0.211 2079 Planarity : 0.004 0.058 2333 Dihedral : 12.964 178.715 2115 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1618 helix: 0.77 (0.19), residues: 756 sheet: -1.20 (0.45), residues: 147 loop : -2.55 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 178 HIS 0.003 0.001 HIS A 451 PHE 0.021 0.001 PHE B 219 TYR 0.042 0.001 TYR A 419 ARG 0.006 0.001 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 578) hydrogen bonds : angle 4.47490 ( 1627) covalent geometry : bond 0.00314 (14034) covalent geometry : angle 0.64159 (18966) *********************** 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 345 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4610 (ttp80) cc_final: 0.3593 (mpp-170) REVERT: A 26 ARG cc_start: 0.5505 (mtt180) cc_final: 0.4846 (tpp-160) REVERT: A 43 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7456 (mm-40) REVERT: A 128 MET cc_start: 0.6425 (mpp) cc_final: 0.6170 (mpp) REVERT: A 267 MET cc_start: 0.7960 (mpp) cc_final: 0.7719 (mtm) REVERT: A 291 PHE cc_start: 0.8466 (m-80) cc_final: 0.7788 (m-10) REVERT: A 354 GLU cc_start: 0.5678 (tp30) cc_final: 0.5403 (tm-30) REVERT: A 423 MET cc_start: 0.7912 (mtt) cc_final: 0.7599 (mtt) REVERT: A 457 PHE cc_start: 0.7962 (m-80) cc_final: 0.7469 (m-80) REVERT: A 549 TYR cc_start: 0.8605 (m-10) cc_final: 0.8355 (m-10) REVERT: B 4 ASN cc_start: 0.8481 (t0) cc_final: 0.7721 (t0) REVERT: B 77 ASN cc_start: 0.8266 (p0) cc_final: 0.7803 (p0) REVERT: B 101 MET cc_start: 0.7273 (pmm) cc_final: 0.6693 (pmm) REVERT: B 138 ARG cc_start: 0.7452 (mtp-110) cc_final: 0.6761 (ttm-80) REVERT: B 166 VAL cc_start: 0.8319 (m) cc_final: 0.7835 (m) REVERT: B 176 MET cc_start: 0.7550 (mtp) cc_final: 0.7258 (mtm) REVERT: B 259 THR cc_start: 0.8409 (p) cc_final: 0.7599 (t) REVERT: B 310 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7861 (mmmt) REVERT: B 335 MET cc_start: 0.7319 (ttm) cc_final: 0.6617 (ttp) REVERT: B 375 MET cc_start: 0.7907 (mtm) cc_final: 0.7316 (mtp) REVERT: B 391 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7243 (pt0) REVERT: B 467 PHE cc_start: 0.9449 (t80) cc_final: 0.9141 (t80) REVERT: B 604 SER cc_start: 0.8949 (m) cc_final: 0.8044 (t) REVERT: B 675 MET cc_start: 0.6236 (ppp) cc_final: 0.5914 (ppp) REVERT: B 682 GLU cc_start: 0.8638 (tt0) cc_final: 0.7907 (tm-30) REVERT: C 9 LYS cc_start: 0.8302 (mttt) cc_final: 0.7647 (ptpp) REVERT: C 186 ILE cc_start: 0.6737 (mm) cc_final: 0.6282 (mm) REVERT: C 225 LEU cc_start: 0.8276 (mt) cc_final: 0.7958 (mt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2412 time to fit residues: 123.5050 Evaluate side-chains 273 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN C 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126537 restraints weight = 23321.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129077 restraints weight = 15543.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130588 restraints weight = 11589.008| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14034 Z= 0.135 Angle : 0.645 8.681 18966 Z= 0.325 Chirality : 0.043 0.215 2079 Planarity : 0.004 0.058 2333 Dihedral : 12.983 179.008 2115 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 0.14 % Allowed : 0.62 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1618 helix: 0.76 (0.19), residues: 756 sheet: -1.19 (0.45), residues: 147 loop : -2.55 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 178 HIS 0.003 0.001 HIS B 660 PHE 0.022 0.001 PHE A 42 TYR 0.014 0.001 TYR C 104 ARG 0.005 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 578) hydrogen bonds : angle 4.51790 ( 1627) covalent geometry : bond 0.00302 (14034) covalent geometry : angle 0.64488 (18966) *********************** 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 334 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4605 (ttp80) cc_final: 0.3596 (mpp-170) REVERT: A 26 ARG cc_start: 0.5450 (mtt180) cc_final: 0.4884 (tpp-160) REVERT: A 43 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7448 (mm110) REVERT: A 128 MET cc_start: 0.6448 (mpp) cc_final: 0.5810 (mpp) REVERT: A 291 PHE cc_start: 0.8560 (m-80) cc_final: 0.7697 (m-10) REVERT: A 323 LYS cc_start: 0.8429 (ptpt) cc_final: 0.7913 (tttt) REVERT: A 354 GLU cc_start: 0.5571 (tp30) cc_final: 0.5263 (tm-30) REVERT: A 408 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6346 (tp30) REVERT: A 419 TYR cc_start: 0.7157 (t80) cc_final: 0.6891 (t80) REVERT: A 424 CYS cc_start: 0.7108 (t) cc_final: 0.6851 (t) REVERT: A 457 PHE cc_start: 0.8040 (m-80) cc_final: 0.7540 (m-80) REVERT: A 549 TYR cc_start: 0.8642 (m-10) cc_final: 0.8435 (m-10) REVERT: A 578 GLU cc_start: 0.7768 (tt0) cc_final: 0.7439 (tt0) REVERT: A 629 VAL cc_start: 0.8708 (t) cc_final: 0.8506 (t) REVERT: A 680 CYS cc_start: 0.8174 (t) cc_final: 0.7477 (t) REVERT: B 4 ASN cc_start: 0.8398 (t0) cc_final: 0.7857 (t0) REVERT: B 77 ASN cc_start: 0.8287 (p0) cc_final: 0.7780 (p0) REVERT: B 101 MET cc_start: 0.7407 (pmm) cc_final: 0.6709 (pmm) REVERT: B 138 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.6829 (ttm-80) REVERT: B 166 VAL cc_start: 0.8336 (m) cc_final: 0.7778 (m) REVERT: B 172 ILE cc_start: 0.9082 (mm) cc_final: 0.8795 (mm) REVERT: B 176 MET cc_start: 0.7503 (mtp) cc_final: 0.7212 (mtm) REVERT: B 310 LYS cc_start: 0.8258 (mmtp) cc_final: 0.7882 (mmmt) REVERT: B 335 MET cc_start: 0.7329 (ttm) cc_final: 0.6598 (ttp) REVERT: B 375 MET cc_start: 0.7625 (mtm) cc_final: 0.6916 (mtp) REVERT: B 547 MET cc_start: 0.8587 (mmt) cc_final: 0.8267 (tpp) REVERT: B 604 SER cc_start: 0.8946 (m) cc_final: 0.7953 (t) REVERT: B 675 MET cc_start: 0.6965 (ppp) cc_final: 0.6560 (ppp) REVERT: C 9 LYS cc_start: 0.8262 (mttt) cc_final: 0.7805 (mtpp) REVERT: C 186 ILE cc_start: 0.6696 (mm) cc_final: 0.6290 (mm) REVERT: C 225 LEU cc_start: 0.8197 (mt) cc_final: 0.7934 (mt) outliers start: 2 outliers final: 1 residues processed: 333 average time/residue: 0.3092 time to fit residues: 154.4792 Evaluate side-chains 269 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 140 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131183 restraints weight = 23226.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133686 restraints weight = 15940.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135841 restraints weight = 10784.563| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14034 Z= 0.126 Angle : 0.653 10.285 18966 Z= 0.327 Chirality : 0.042 0.213 2079 Planarity : 0.004 0.057 2333 Dihedral : 12.979 179.752 2115 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1618 helix: 0.80 (0.19), residues: 754 sheet: -1.17 (0.45), residues: 147 loop : -2.45 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 178 HIS 0.002 0.001 HIS B 660 PHE 0.019 0.001 PHE B 413 TYR 0.015 0.001 TYR A 419 ARG 0.010 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 578) hydrogen bonds : angle 4.51714 ( 1627) covalent geometry : bond 0.00284 (14034) covalent geometry : angle 0.65331 (18966) ********************** 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 339 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4448 (ttp80) cc_final: 0.3443 (mpp-170) REVERT: A 26 ARG cc_start: 0.5721 (mtt180) cc_final: 0.5014 (tpp-160) REVERT: A 43 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7248 (mm-40) REVERT: A 128 MET cc_start: 0.6401 (mpp) cc_final: 0.5891 (mpp) REVERT: A 291 PHE cc_start: 0.8419 (m-80) cc_final: 0.7830 (m-10) REVERT: A 323 LYS cc_start: 0.8237 (ptpt) cc_final: 0.7932 (tttt) REVERT: A 408 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6093 (tp30) REVERT: A 409 MET cc_start: 0.7480 (tpt) cc_final: 0.7015 (ttm) REVERT: A 419 TYR cc_start: 0.7629 (t80) cc_final: 0.7076 (t80) REVERT: A 423 MET cc_start: 0.8061 (mtm) cc_final: 0.7302 (mtt) REVERT: A 457 PHE cc_start: 0.7986 (m-80) cc_final: 0.7551 (m-80) REVERT: A 578 GLU cc_start: 0.7788 (tt0) cc_final: 0.7176 (tt0) REVERT: A 590 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 653 LEU cc_start: 0.8277 (mp) cc_final: 0.8004 (mp) REVERT: B 4 ASN cc_start: 0.8431 (t0) cc_final: 0.7922 (t0) REVERT: B 77 ASN cc_start: 0.8187 (p0) cc_final: 0.7716 (p0) REVERT: B 101 MET cc_start: 0.7678 (pmm) cc_final: 0.6858 (pmm) REVERT: B 138 ARG cc_start: 0.7496 (mtp-110) cc_final: 0.6865 (ttm-80) REVERT: B 166 VAL cc_start: 0.8219 (m) cc_final: 0.7783 (m) REVERT: B 176 MET cc_start: 0.7518 (mtp) cc_final: 0.7244 (mtm) REVERT: B 391 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7414 (pt0) REVERT: B 446 ASP cc_start: 0.7543 (p0) cc_final: 0.7141 (t0) REVERT: B 604 SER cc_start: 0.8855 (m) cc_final: 0.7931 (t) REVERT: C 9 LYS cc_start: 0.8099 (mttt) cc_final: 0.7700 (mtpp) REVERT: C 186 ILE cc_start: 0.6659 (mm) cc_final: 0.6323 (mm) REVERT: C 225 LEU cc_start: 0.8206 (mt) cc_final: 0.7933 (mt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3069 time to fit residues: 156.5263 Evaluate side-chains 272 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 88 optimal weight: 0.9980 chunk 159 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 110 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS A 451 HIS A 638 ASN B 296 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 = 0.3905 r_free = 0.3905 target = 0.159095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132412 restraints weight = 23272.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134819 restraints weight = 15535.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136308 restraints weight = 11612.002| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14034 Z= 0.123 Angle : 0.652 8.839 18966 Z= 0.328 Chirality : 0.042 0.214 2079 Planarity : 0.004 0.057 2333 Dihedral : 12.953 179.376 2115 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 0.14 % Allowed : 0.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1618 helix: 0.79 (0.19), residues: 754 sheet: -1.16 (0.45), residues: 144 loop : -2.44 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 178 HIS 0.004 0.001 HIS A 451 PHE 0.020 0.001 PHE B 219 TYR 0.018 0.001 TYR A 419 ARG 0.016 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 578) hydrogen bonds : angle 4.45614 ( 1627) covalent geometry : bond 0.00270 (14034) covalent geometry : angle 0.65160 (18966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5010.48 seconds wall clock time: 91 minutes 44.74 seconds (5504.74 seconds total)