Starting phenix.real_space_refine on Wed Mar 4 03:36:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmj_13536/03_2026/7pmj_13536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmj_13536/03_2026/7pmj_13536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pmj_13536/03_2026/7pmj_13536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmj_13536/03_2026/7pmj_13536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pmj_13536/03_2026/7pmj_13536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmj_13536/03_2026/7pmj_13536.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6421 2.51 5 N 1713 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10085 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 6001 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 27, 'TRANS': 706} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.24, per 1000 atoms: 0.22 Number of scatterers: 10085 At special positions: 0 Unit cell: (102.3, 138.6, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1880 8.00 N 1713 7.00 C 6421 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 537.9 milliseconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 15 sheets defined 55.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.163A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 66 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.874A pdb=" N ALA A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.762A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.891A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.517A pdb=" N ARG A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.273A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 271 No H-bonds generated for 'chain 'A' and resid 270 through 271' Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.639A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.943A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.808A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.655A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.909A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.505A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.895A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.507A pdb=" N ILE A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.797A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 4.070A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.779A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.969A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.509A pdb=" N HIS A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.715A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.799A pdb=" N ARG A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 715 removed outlier: 3.750A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.622A pdb=" N TRP A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.963A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.562A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.037A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.544A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 268 Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.312A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.636A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.271A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 15 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.568A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.652A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.599A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.514A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.620A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.935A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 523 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1700 1.32 - 1.45: 2743 1.45 - 1.57: 5744 1.57 - 1.70: 9 1.70 - 1.83: 102 Bond restraints: 10298 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.444 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.453 0.072 2.10e-02 2.27e+03 1.16e+01 ... (remaining 10293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.79: 13878 5.79 - 11.58: 29 11.58 - 17.36: 3 17.36 - 23.15: 1 23.15 - 28.94: 1 Bond angle restraints: 13912 Sorted by residual: angle pdb=" CB MET A 783 " pdb=" CG MET A 783 " pdb=" SD MET A 783 " ideal model delta sigma weight residual 112.70 141.64 -28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.92 10.78 1.80e+00 3.09e-01 3.58e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 101.59 8.51 1.90e+00 2.77e-01 2.01e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.03 4.37 1.00e+00 1.00e+00 1.91e+01 ... (remaining 13907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 5955 26.62 - 53.24: 204 53.24 - 79.86: 52 79.86 - 106.48: 14 106.48 - 133.10: 3 Dihedral angle restraints: 6228 sinusoidal: 2574 harmonic: 3654 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.90 133.10 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" CA ALA A 554 " pdb=" C ALA A 554 " pdb=" N ASP A 555 " pdb=" CA ASP A 555 " ideal model delta harmonic sigma weight residual 180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 57.12 -117.12 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1070 0.061 - 0.121: 368 0.121 - 0.182: 73 0.182 - 0.243: 5 0.243 - 0.303: 3 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1516 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.002 2.00e-02 2.50e+03 4.21e-02 3.54e+01 pdb=" CG TYR C 306 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.061 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 784 " 0.108 9.50e-02 1.11e+02 6.58e-02 2.61e+01 pdb=" NE ARG A 784 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 784 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG A 784 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 784 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 711 " 0.008 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR A 711 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 711 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 711 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 711 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 711 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR A 711 " -0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 711 " 0.042 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 18 2.36 - 3.00: 5569 3.00 - 3.63: 14884 3.63 - 4.27: 22628 4.27 - 4.90: 37944 Nonbonded interactions: 81043 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.729 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.867 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 1.947 2.170 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1902 " model vdw 2.042 2.170 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.158 3.120 ... (remaining 81038 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 individual isotropic 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: 2.310 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.010 0.151 10300 Z= 0.430 Angle : 1.116 28.938 13918 Z= 0.624 Chirality : 0.061 0.303 1519 Planarity : 0.008 0.066 1772 Dihedral : 15.905 133.101 3866 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.20), residues: 1220 helix: -1.98 (0.16), residues: 613 sheet: -0.23 (0.38), residues: 160 loop : -0.33 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.011 ARG A 784 TYR 0.068 0.008 TYR A 742 PHE 0.051 0.003 PHE A 564 TRP 0.073 0.006 TRP A 484 HIS 0.009 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00982 (10298) covalent geometry : angle 1.11426 (13912) hydrogen bonds : bond 0.16115 ( 521) hydrogen bonds : angle 7.39590 ( 1449) link_TRANS : bond 0.01797 ( 2) link_TRANS : angle 3.53122 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8976 (p0) cc_final: 0.8703 (p0) REVERT: C 47 MET cc_start: 0.6922 (mmm) cc_final: 0.6433 (tpp) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1375 time to fit residues: 17.1219 Evaluate side-chains 57 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 75 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 264 GLN A 354 HIS A 463 GLN A 642 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 296 ASN C 371 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.056315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.039342 restraints weight = 59270.260| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.70 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10300 Z= 0.141 Angle : 0.658 8.225 13918 Z= 0.346 Chirality : 0.043 0.195 1519 Planarity : 0.004 0.044 1772 Dihedral : 9.553 119.756 1415 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.75 % Allowed : 2.89 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1220 helix: 0.55 (0.20), residues: 617 sheet: 0.65 (0.42), residues: 143 loop : 0.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 343 TYR 0.026 0.001 TYR A 742 PHE 0.013 0.001 PHE B 96 TRP 0.033 0.002 TRP A 781 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00301 (10298) covalent geometry : angle 0.65771 (13912) hydrogen bonds : bond 0.03996 ( 521) hydrogen bonds : angle 5.21793 ( 1449) link_TRANS : bond 0.00147 ( 2) link_TRANS : angle 0.87118 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.2559 (OUTLIER) cc_final: 0.2047 (ptm) REVERT: A 135 MET cc_start: 0.8180 (mtp) cc_final: 0.7711 (ttm) REVERT: A 478 MET cc_start: 0.8963 (tmm) cc_final: 0.8692 (tmm) REVERT: C 355 MET cc_start: 0.9034 (mpp) cc_final: 0.8497 (mpp) outliers start: 8 outliers final: 2 residues processed: 68 average time/residue: 0.1145 time to fit residues: 10.9027 Evaluate side-chains 55 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 484 TRP Chi-restraints excluded: chain A residue 715 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 410 ASN C 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.056583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039785 restraints weight = 59066.623| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.63 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10300 Z= 0.107 Angle : 0.550 8.455 13918 Z= 0.286 Chirality : 0.040 0.201 1519 Planarity : 0.004 0.040 1772 Dihedral : 8.087 119.962 1414 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.37 % Allowed : 5.04 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1220 helix: 1.34 (0.21), residues: 623 sheet: 0.88 (0.42), residues: 150 loop : 0.52 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.021 0.001 TYR A 742 PHE 0.014 0.001 PHE B 96 TRP 0.025 0.002 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00229 (10298) covalent geometry : angle 0.55046 (13912) hydrogen bonds : bond 0.03274 ( 521) hydrogen bonds : angle 4.77776 ( 1449) link_TRANS : bond 0.00153 ( 2) link_TRANS : angle 0.60797 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.442 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: B 73 MET cc_start: 0.1996 (OUTLIER) cc_final: 0.1599 (ptm) REVERT: A 478 MET cc_start: 0.8967 (tmm) cc_final: 0.8659 (tmm) REVERT: A 648 MET cc_start: 0.9199 (mmm) cc_final: 0.8900 (mmm) REVERT: C 47 MET cc_start: 0.6721 (mmm) cc_final: 0.6327 (mmm) REVERT: C 313 MET cc_start: 0.8712 (mmm) cc_final: 0.8345 (tpt) REVERT: C 355 MET cc_start: 0.9020 (mpp) cc_final: 0.8475 (mpp) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 0.1129 time to fit residues: 9.6326 Evaluate side-chains 52 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 715 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS B 147 HIS ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.055694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038912 restraints weight = 59158.993| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.71 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10300 Z= 0.128 Angle : 0.551 8.300 13918 Z= 0.281 Chirality : 0.040 0.191 1519 Planarity : 0.004 0.039 1772 Dihedral : 7.881 118.502 1414 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.47 % Allowed : 6.53 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1220 helix: 1.67 (0.22), residues: 621 sheet: 0.77 (0.41), residues: 163 loop : 0.53 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.018 0.001 TYR A 742 PHE 0.010 0.001 PHE A 441 TRP 0.021 0.002 TRP A 781 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00282 (10298) covalent geometry : angle 0.55052 (13912) hydrogen bonds : bond 0.03220 ( 521) hydrogen bonds : angle 4.67038 ( 1449) link_TRANS : bond 0.00169 ( 2) link_TRANS : angle 0.64622 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.2095 (OUTLIER) cc_final: 0.1772 (ptm) REVERT: A 135 MET cc_start: 0.8222 (mtp) cc_final: 0.7864 (ttm) REVERT: A 478 MET cc_start: 0.9029 (tmm) cc_final: 0.8752 (tmm) REVERT: A 742 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.6512 (p90) REVERT: C 355 MET cc_start: 0.9017 (mpp) cc_final: 0.8508 (mpp) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.0953 time to fit residues: 7.9037 Evaluate side-chains 53 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 742 TYR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.054817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037937 restraints weight = 59680.509| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 4.74 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10300 Z= 0.156 Angle : 0.552 8.502 13918 Z= 0.281 Chirality : 0.040 0.194 1519 Planarity : 0.004 0.039 1772 Dihedral : 7.852 117.601 1414 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.84 % Allowed : 7.09 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1220 helix: 1.76 (0.22), residues: 620 sheet: 0.80 (0.41), residues: 159 loop : 0.41 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 792 TYR 0.019 0.001 TYR A 742 PHE 0.010 0.001 PHE B 96 TRP 0.020 0.002 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00346 (10298) covalent geometry : angle 0.55241 (13912) hydrogen bonds : bond 0.03310 ( 521) hydrogen bonds : angle 4.68741 ( 1449) link_TRANS : bond 0.00211 ( 2) link_TRANS : angle 0.62130 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.2265 (OUTLIER) cc_final: 0.1414 (ptm) REVERT: A 135 MET cc_start: 0.8146 (mtp) cc_final: 0.7914 (ttm) REVERT: A 323 MET cc_start: 0.9038 (tpp) cc_final: 0.8772 (tpp) REVERT: A 382 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9098 (p) REVERT: A 478 MET cc_start: 0.9096 (tmm) cc_final: 0.8833 (tmm) REVERT: A 742 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6407 (p90) REVERT: C 355 MET cc_start: 0.8983 (mpp) cc_final: 0.8513 (mpp) outliers start: 9 outliers final: 3 residues processed: 56 average time/residue: 0.0961 time to fit residues: 7.9547 Evaluate side-chains 52 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 742 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.054616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.037630 restraints weight = 60216.454| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.77 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10300 Z= 0.179 Angle : 0.575 8.920 13918 Z= 0.291 Chirality : 0.041 0.192 1519 Planarity : 0.004 0.039 1772 Dihedral : 7.905 118.477 1414 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.75 % Allowed : 8.58 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1220 helix: 1.80 (0.21), residues: 622 sheet: 0.74 (0.41), residues: 160 loop : 0.26 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 792 TYR 0.018 0.001 TYR A 742 PHE 0.011 0.001 PHE B 96 TRP 0.018 0.002 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00398 (10298) covalent geometry : angle 0.57517 (13912) hydrogen bonds : bond 0.03410 ( 521) hydrogen bonds : angle 4.72090 ( 1449) link_TRANS : bond 0.00263 ( 2) link_TRANS : angle 0.61785 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.1747 (OUTLIER) cc_final: 0.1261 (ptm) REVERT: A 135 MET cc_start: 0.8119 (mtp) cc_final: 0.7899 (ttm) REVERT: A 382 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9056 (p) REVERT: A 478 MET cc_start: 0.9073 (tmm) cc_final: 0.8823 (tmm) REVERT: C 355 MET cc_start: 0.9032 (mpp) cc_final: 0.8560 (mpp) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.0891 time to fit residues: 7.4592 Evaluate side-chains 50 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 0.0470 chunk 105 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.055677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.039030 restraints weight = 59309.326| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.57 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10300 Z= 0.095 Angle : 0.517 9.154 13918 Z= 0.260 Chirality : 0.039 0.184 1519 Planarity : 0.003 0.038 1772 Dihedral : 7.587 115.146 1414 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.47 % Allowed : 8.96 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.25), residues: 1220 helix: 2.01 (0.22), residues: 621 sheet: 0.86 (0.42), residues: 158 loop : 0.33 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.013 0.001 TYR A 742 PHE 0.007 0.001 PHE B 96 TRP 0.016 0.001 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00203 (10298) covalent geometry : angle 0.51719 (13912) hydrogen bonds : bond 0.02846 ( 521) hydrogen bonds : angle 4.46217 ( 1449) link_TRANS : bond 0.00121 ( 2) link_TRANS : angle 0.64262 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 73 MET cc_start: 0.1275 (OUTLIER) cc_final: 0.0645 (ptm) REVERT: A 323 MET cc_start: 0.9020 (tpp) cc_final: 0.8753 (tpp) REVERT: A 478 MET cc_start: 0.9012 (tmm) cc_final: 0.8792 (tmm) REVERT: C 225 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8967 (t0) REVERT: C 313 MET cc_start: 0.9042 (mmm) cc_final: 0.8764 (tpp) REVERT: C 355 MET cc_start: 0.8967 (mpp) cc_final: 0.8495 (mpp) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.0855 time to fit residues: 7.4042 Evaluate side-chains 51 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.055385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.038656 restraints weight = 59263.289| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.60 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10300 Z= 0.124 Angle : 0.541 9.914 13918 Z= 0.269 Chirality : 0.040 0.187 1519 Planarity : 0.003 0.038 1772 Dihedral : 7.591 116.322 1414 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.65 % Allowed : 9.51 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.24), residues: 1220 helix: 2.00 (0.22), residues: 621 sheet: 0.86 (0.42), residues: 158 loop : 0.30 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.015 0.001 TYR A 742 PHE 0.010 0.001 PHE B 96 TRP 0.016 0.001 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00274 (10298) covalent geometry : angle 0.54055 (13912) hydrogen bonds : bond 0.02986 ( 521) hydrogen bonds : angle 4.49948 ( 1449) link_TRANS : bond 0.00158 ( 2) link_TRANS : angle 0.64606 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.0804 (OUTLIER) cc_final: 0.0410 (ptm) REVERT: A 478 MET cc_start: 0.9039 (tmm) cc_final: 0.8820 (tmm) REVERT: A 742 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6380 (p90) REVERT: C 47 MET cc_start: 0.8180 (ppp) cc_final: 0.7922 (ppp) REVERT: C 123 MET cc_start: 0.9350 (tpt) cc_final: 0.8969 (tpt) REVERT: C 225 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8939 (t0) REVERT: C 355 MET cc_start: 0.8974 (mpp) cc_final: 0.8508 (mpp) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.0841 time to fit residues: 7.0640 Evaluate side-chains 53 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 742 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.0070 chunk 106 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.055533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038819 restraints weight = 59521.117| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.70 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10300 Z= 0.100 Angle : 0.516 9.872 13918 Z= 0.257 Chirality : 0.039 0.185 1519 Planarity : 0.003 0.037 1772 Dihedral : 7.473 115.504 1414 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.75 % Allowed : 9.42 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1220 helix: 2.07 (0.22), residues: 615 sheet: 0.91 (0.42), residues: 158 loop : 0.30 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.013 0.001 TYR A 742 PHE 0.007 0.001 PHE C 255 TRP 0.016 0.001 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00218 (10298) covalent geometry : angle 0.51626 (13912) hydrogen bonds : bond 0.02786 ( 521) hydrogen bonds : angle 4.39560 ( 1449) link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.64469 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.1010 (OUTLIER) cc_final: 0.0655 (ptm) REVERT: A 177 MET cc_start: 0.8986 (ptm) cc_final: 0.8453 (ppp) REVERT: A 323 MET cc_start: 0.9052 (tpp) cc_final: 0.8777 (tpp) REVERT: A 467 MET cc_start: 0.8624 (tmm) cc_final: 0.8134 (tmm) REVERT: A 478 MET cc_start: 0.9107 (tmm) cc_final: 0.8906 (tmm) REVERT: C 47 MET cc_start: 0.8125 (ppp) cc_final: 0.7797 (ppp) REVERT: C 225 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8961 (t0) REVERT: C 313 MET cc_start: 0.9040 (mmm) cc_final: 0.8809 (tpp) REVERT: C 355 MET cc_start: 0.8997 (mpp) cc_final: 0.8512 (mpp) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.0732 time to fit residues: 6.5453 Evaluate side-chains 55 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 270 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.055587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038894 restraints weight = 58636.721| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.61 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10300 Z= 0.113 Angle : 0.541 10.220 13918 Z= 0.267 Chirality : 0.040 0.186 1519 Planarity : 0.003 0.037 1772 Dihedral : 7.467 115.702 1414 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.75 % Allowed : 9.98 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.25), residues: 1220 helix: 2.09 (0.22), residues: 621 sheet: 0.95 (0.42), residues: 158 loop : 0.27 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.014 0.001 TYR A 742 PHE 0.008 0.001 PHE B 16 TRP 0.017 0.002 TRP A 781 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00252 (10298) covalent geometry : angle 0.54104 (13912) hydrogen bonds : bond 0.02890 ( 521) hydrogen bonds : angle 4.44340 ( 1449) link_TRANS : bond 0.00145 ( 2) link_TRANS : angle 0.63640 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.0572 (OUTLIER) cc_final: 0.0266 (ptm) REVERT: A 323 MET cc_start: 0.8996 (tpp) cc_final: 0.8717 (tpp) REVERT: A 467 MET cc_start: 0.8597 (tmm) cc_final: 0.8218 (tmm) REVERT: A 478 MET cc_start: 0.9127 (tmm) cc_final: 0.8915 (tmm) REVERT: C 47 MET cc_start: 0.8205 (ppp) cc_final: 0.7817 (ppp) REVERT: C 225 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8956 (t0) REVERT: C 355 MET cc_start: 0.8967 (mpp) cc_final: 0.8505 (mpp) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.0798 time to fit residues: 6.8899 Evaluate side-chains 57 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 270 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 88 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.055596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039096 restraints weight = 59061.018| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.61 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10300 Z= 0.097 Angle : 0.546 12.807 13918 Z= 0.268 Chirality : 0.039 0.184 1519 Planarity : 0.003 0.037 1772 Dihedral : 7.404 115.051 1414 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.65 % Allowed : 10.26 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1220 helix: 2.06 (0.22), residues: 621 sheet: 1.04 (0.43), residues: 158 loop : 0.28 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.013 0.001 TYR A 742 PHE 0.007 0.001 PHE C 255 TRP 0.016 0.001 TRP A 781 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00212 (10298) covalent geometry : angle 0.54630 (13912) hydrogen bonds : bond 0.02766 ( 521) hydrogen bonds : angle 4.42207 ( 1449) link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.64792 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.77 seconds wall clock time: 32 minutes 59.28 seconds (1979.28 seconds total)